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On the Thermal Behavior during Spatial Anisotropic Femtoseconds Laser-

DNA Interaction: The Crucial Role of Hermite Polynomials

Article in Materials · April 2023

DOI: 10.3390/ma16093334

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 materials
Article
On the Thermal Behavior during Spatial Anisotropic
Femtoseconds Laser-DNA Interaction: The Crucial Role
of Hermite Polynomials
Mihai Oane , Cristian Nicolae Mihailescu * and Alexandra Maria Isabel Trefilov *

National Institute for Laser, Plasma and Radiation Physics, 077125 Măgurele, Romania
* Correspondence: [email protected] (C.N.M.); [email protected] (A.M.I.T.)

Abstract: A novel analytical formalism based on the quantum heat transport equation is proposed
for the interaction of fs-laser pulses with deoxyribonucleic acid (DNA) strands. The formalism has
the intensity of the laser beam and the interaction time between the laser and the DNA as input
parameters. To this end, the thermal distribution generated in the irradiated DNA strands was
introduced by splitting the laser beam into transverse Hermite-Gauss modes. To achieve this goal,
a new powerful mathematical model was developed and applied. Fluctuations in laser intensity
were taken into account by modeling them as superpositions of Hermite-Gauss laser modes. These
analyses were carried out for a laser pulse duration of 100 fs, where a tiny heat-affected zone is
expected, with positive predicted effects on the stability and repeatability of this technology. The
main conclusion is that the laser beam spatial distribution intensity plays an essential role in the
generation of the shape and magnitude of the thermal field at the junction of the irradiated DNA
strands. The model may prove useful in modeling laser beam processing under significant intensity
fluctuations. There are at least two main areas of application for the present model of heat transfer
from laser to DNA: (i) the study of DNA elongation without destroying the target information (for
a sample temperature variation lower than 10 K; in the case of H[1,y]); and (ii) cancer treatment
(especially of skin tissue), where we should obtain a temperature variation higher than 10 K (but
lower than 30 K; in the case of H[2,y], H[4,y]), in order to eradicate the diseased cells.
Citation: Oane, M.; Mihailescu, C.N.;
Trefilov, A.M.I. On the Thermal Keywords: deoxyribonucleic acid; Hermite-Gauss laser modes; fs laser pulses; heat equation; DNA
Behavior during Spatial Anisotropic elongation; cancer treatment
Femtoseconds Laser-DNA
Interaction: The Crucial Role of
Hermite Polynomials. Materials 2023,
16, 3334. https://doi.org/10.3390/
1. Introduction
ma16093334
DNA is an organic polymer composed of a sugar (deoxyribose)-phosphate back-
Academic Editor: Halina Kaczmarek bone and four nitrogenous base subunits: guanine (G), cytosine (C), adenine (A), and
Received: 16 March 2023
thymine (T). The subunits, called nucleotide monomers, are connected by strong electro-
Revised: 14 April 2023
magnetic attractions [1]. The structure of DNA, as depicted in the Watson and Crick model,
Accepted: 20 April 2023 is a double-stranded, antiparallel, right-handed helix. The sugar-phosphate backbones
Published: 24 April 2023 of the DNA strands form the exterior of the helix, while the nitrogenous bases are on the
inside, forming hydrogen-bonded pairs that hold the DNA strands together. [2]. Thus, the
DNA double helix is stabilized by two main forces: hydrogen bonds between nucleotides
and base nucleotides and base-stacking interactions between aromatic nucleobases [3].
Copyright: © 2023 by the authors. The Watson and Crick model explains the complementarity of the base sequences on
Licensee MDPI, Basel, Switzerland. the two strands and, implicitly, the heritability of genetic information and the transcription
This article is an open access article of genetic information, but it does not consider other advantages, such as information
distributed under the terms and accessibility and packaging.
conditions of the Creative Commons Today, other molecular simulation models of nucleic acids are well established, cov-
Attribution (CC BY) license (https://
ering a wide range of information, while modeling techniques are a powerful tool for
creativecommons.org/licenses/by/
describing them. All these models are required to follow two rules: (i) the models should
4.0/).

Materials 2023, 16, 3334. https://doi.org/10.3390/ma16093334 https://www.mdpi.com/journal/materials

Materials 2023, 16, 3334 2 of 14

be consistent with the physical rules that govern the structure of molecules, and (ii) they
should explain all the experimental information that is available [4,5].
DNA models can be better understood by studying molecular electronics, the ‘making’
of electronics at the molecular level, which can be used as a computational tool in its own
right. Clearly, molecular electronics belong to an area of science in which mathematical
modeling and simulations are powerful tools for classical, semi-classical, and microscopic
level calculations. The studies show that the models cleverly mix macroscopic and micro-
scopic notions at the semi-classical level, which is also the focus of this paper. Indeed, there
is a junction between classical notions (such as the heat transport equation) and those of
quantum mechanics at the level of a few or single molecules [6,7].
In this regard, the study of DNA involves three levels of study: classical (macroscopic),
semi-classical, and microscopic (quantum). Classical models assume that DNA is an ideal
rod that obeys macroscopic laws. However, these models do not take into account the
sequence structure of DNA.
The semi-classical approach assumes that many small rods form a normal rod. These
small rods are entitled beads. They interact individually with external forces.
Semi-classical models allow experimental data on polynucleotides to be linked to their
macroscopic properties. From a theoretical point of view, we can use semi-classical heat
equations with quantum “ingredients”. The model presented in the present study can be
regarded as a semi-classical approach to the thermal effects of laser-DNA interaction [8].
At the molecular scale, the heat and charge transport phenomena through molecules
can be regarded as quantum phenomena, where the electrons are the charge and heat
carriers [9,10]. Many experiments have been carried out in which an electric current is
passed between two metallic electrodes via a single-layer molecular film [11–13]. The
transport phenomena can be examined by scanning tunneling microscopy with a single or
a few molecules on a gold surface, with the tip acting as a counter electrode [14,15]. Several
studies have been carried out on the current through a single molecule, with the connection
to both electrodes placed symmetrically to a well-defined chemical bond, allowing the
function to remain mechanically stable even at room temperature [16,17]. However, all
these studies must take into account the irreversible chemical damage produced in the
DNA’s internal structure due to abnormal factors. One of these factors is temperature;
above 190 ◦ C, complete DNA degradation takes place [18].
Lately, ultrafast laser pulse excitation has been used to generate highly localized
temperature elevations capable of controlling transport phenomena in single chemical
molecules and hydrogen molecules [11,19,20]. It is therefore necessary for the models to be
able to image processes at the atomic level. The first measurements of dynamic processes
deep inside an atom were carried out using ultrafast spectroscopy [21]. In this context,
the paper introduces the thermal evolution in the case of laser-DNA interaction using a
new approach based on Hermite polynomials. It is known that there is always a zone
surrounding laser irradiation spots, called the heat-affected zone (HAZ), where either metal
or thermoplastics, or smaller proportions of other materials, are not melted, even though
their microstructure and properties change [22]. The heat from the welding process and
subsequent cooling cause this change from the weld interface to the end of the HAZ. The
extent and magnitude of the property change depend primarily on the base material and
the amount and concentration of heat input. The thermal diffusivity of the base material
plays a large part in this change—if the diffusivity and the material cooling rate are high,
then the HAZ is relatively small. Alternatively, low diffusivity leads to slower cooling
and a larger HAZ. The amount of heat input reflected in the laser pulse duration plays a
key role in this process, as the shorter the duration of the laser pulse, the smaller the HAZ
extension will be. This makes it of particular interest to carry out laser heating with shorter
and shorter laser pulses, down to the 100 fs limit considered in these studies [23].
On the other hand, a limited, quite small HAZ confers high precision to the laser
processes and high stability to the laser induced processing/heating. The reported results
can be easily reproduced by any laboratory with minimum manufacturing costs. It should
Materials 2023, 16, x FOR PEER REVIEW 3 of 15

Materials 2023, 16, 3334 On the other hand, a limited, quite small HAZ confers high precision to the laser 3 of 14
processes and high stability to the laser induced processing/heating. The reported results
can be easily reproduced by any laboratory with minimum manufacturing costs. It
should
also bealso
noted bethat
noted laserthat laser of
pulses pulses
100 fsofduration
100 fs duration
are availableare available
on the market,on the although
market,
although
much shorter laser pulses (i.e., as) have been reported. This means that this study is inthis
much shorter laser pulses (i.e., as) have been reported. This means that line
study is intrend
with the line with the trend
of research andofprogress
researchinand the progress
field. in the field.
The
Themodel
modelproposed
proposed inin
this paper
this paper could be extended
could be extended to other typestypes
to other of radiation with
of radiation
multiple applications,
with multiple such as those
applications, such used
as thoseto treat
usedcancer. Laser
to treat cancerLaser
cancer. therapy is very
cancer popularis
therapy
because of thebecause
very popular great advantages
of the greatofadvantages
high-energyof particle
high-energy irradiation
particle (with an order
irradiation of
(with
magnitude of MeV), which produces a Bragg peak. As
an order of magnitude of MeV), which produces a Bragg peak. As we have seen, upwe have seen, up until now there have
been
untilmajor
now thereeffortshave
to modelbeen and major understand the interaction
efforts to model between radiation
and understand and biological
the interaction between
targets
radiationsuch andasbiological
cells, tissues, targets andsuchDNA [24–31].
as cells, The and
tissues, first DNA
step [24–31].
in understanding the
The first step
phenomenon
in understanding is to evaluate the cross section
the phenomenon of the irradiation
is to evaluate the crossofsection
biomolecules and establish
of the irradiation of
the mechanism and
biomolecules of theestablish
interaction thewith secondary
mechanism ofelectrons inducedwith
the interaction by the incident radiation.
secondary electrons
The models
induced and methods
by the incident of cross-section evaluation are very few and complex. It is
radiation.
important to remember
The models and methods that in of microscopic
cross-section models, particles
evaluation are obey the rules
very few of quantum
and complex. It is
mechanics.
important to In remember
view of allthat theinabove information,
microscopic models, theparticles
present obey proposal requires
the rules a good
of quantum
mechanics. In view
understanding of how of all
thethe above
target information,respond
biomolecules the present to theproposal requires
temperature a good
increase
understanding
during fs laser pulseof howhitting, the target biomolecules
especially respond electrons,
for low-energy to the temperature
and thus increasea good
during fs laser of
comprehension pulsethe hitting,
binding especially
energies. This for low-energy
contributionelectrons,
thereforeand aimsthus a good com-
to complement
prehension
the existing ofknowledge
the bindingwith energies. This contribution
a completely thereforemathematical
new, powerful aims to complement model the to
existing knowledge with a completely new, powerful
elucidate and explain the thermal behavior under irradiation. The model describes themathematical model to elucidate
and explain
interaction ofthe thermal (fs)
ultra-short behavior underof
laser beams irradiation.
asymmetric The model describes
moderate intensity with the interaction
the DNA
molecules to analyze the thermal changes and proposes a model to eradicate themolecules
of ultra-short (fs) laser beams of asymmetric moderate intensity with the DNA diseased
to analyzecancer
localized the thermal
cells that changes
showand no proposes
signs of ahavingmodel spread.
to eradicateHere,thethediseased
thermallocalized
waves
cancer cells
generated thatirradiated
in the show no DNA signs strands
of having werespread.
analyzed Here,by the thermal the
considering waves lasergenerated
beam in
in theof
terms irradiated
decoupled DNA strands Hermite-Gauss
transverse were analyzed by considering
modes. The model the laser beamto
was used inderive
terms of a
highly accurate formula to describe the temperature field in DNA samples during fshighly
decoupled transverse Hermite-Gauss modes. The model was used to derive a laser
accurate formula
irradiation. The model to describe the temperature
is simplified and does not field
takein into
DNA samples
account theduring
internal fs structure
laser irra-
diation. The model is simplified and does not take into
of DNA, as no significant modifications are expected when the results are compared withaccount the internal structure of
DNA, as no significant modifications are expected when
nucleotide sequences with enriched cytosine-guanine or adenine-thymine partitions. In the results are compared with
nucleotide
addition, thesequences
model has with enriched
a fast simulationcytosine-guanine
time of less than or adenine-thymine
1 min, and can partitions.be easily
In addition, the model has a fast
adapted for more complex biological simulations. simulation time of less than 1 min, and can be easily
adapted for more complex biological simulations.
2. Mathematical Modeling
2. Mathematical Modeling
A schematic of the interaction between a laser and two strands of DNA is shown in
A schematic of the interaction between a laser and two strands of DNA is shown in
Figure 1. Although DNA molecules are symmetrical along the y and z axes, the system
Figure 1. Although DNA molecules are symmetrical along the y and z axes, the system
behaves asymmetrically because the direction of the laser beam propagation is along the
behaves asymmetrically because the direction of the laser beam propagation is along the
z-axis.
z-axis.ItItisisassumed
assumedthat
thatthe
thelaser
laserbeam
beamisisincident
incidentatatthe
thecenter
centerof
ofthe
thetwo
twoDNA
DNAstrands,
strands,
while the laser beam is stationary at the given point.
while the laser beam is stationary at the given point.

Figure 1. Schematic representation of the interaction between a laser beam and DNA.
Materials 2023, 16, 3334 4 of 14

The application of the quantum heat transport equation [32] is extended to the study
of heat generation and transport in DNA structures by ultra-short laser pulses. Specifically,
a new algebraic approach has been used regarding the polynomial decomposition of
Hermite-Gauss modes:

T ( x, y, z, 0) ∝ ∑ ∑ F × f 1 ( x ) × f 2 (y) × f 3 (z) (1)

m n

where: " √ !#2   2 2

2x x
f 1 ( x ) ≡ Hm × exp − (2)
w w2
" √ !#2   2 2
2y y
f 2 ( y ) ≡ Hn × exp − (3)
w w2

f 3 (z) ≡ exp[−αz] (4)

√  √ 
2y
where x, y, z, and t stand for Cartesian coordinates and, respectively, time; Hm w2x ; Hn w :
are Hermite polynomials of m and n orders, respectively; T represents the temperature increase
rather than the absolute one; F is the laser fluence and w is the 1/e radius of the laser spot (also
known as the laser beam waist, w = wx = wy ), and α designates the absorption coefficient
in the case of the laser-DNA interaction, which is assumed, in a first approximation, to be
equal to the laser-water absorption coefficient.
According to the general mathematical theory of Hermite polynomials for m and
n integers:
Hm ( x ) = am xm + am−2 xm−2 + · · · + a2 x2 + a0 (5)

H2m ( x ) = a2m x2m + · · · + a20 (6)

Hn ( x ) = an xn + an−2 xn−2 + · · · + a1 x (7)

H2n ( x ) = a2n x2n + · · · + 2a1 a3 x4 + a21 x2 (8)

In Equations (5)–(8), the coefficients am , . . . , a2 , a0 , an , . . . , a3 and a1 are real integers.
It is easy to check that both the Gaussian and the constant (and quasi-constant) parts
of the Hermite polynomials have circular symmetry. This follows from Equations (1)–(8),
assuming that x, y, z, and w  1.
For the numerical simulations, we considered that: y and z are in the range [−1, 1] µm,
and w = 2 µm.
According to the current literature, the diameter of DNA molecules covers a rather
large range, from several nm to tens of µm, as it is thought to contain several random coil
conformations in solution due to entropic elasticity and thus contain a number of more
than 7000 DNA double strands [23]. The model therefore assumes that the length of the
DNA molecule is 50 µm.
It is presumed that the center of the laser beam (x, y, z) = (0, 0, 0) interacts with the
DNA at the junction of the strands. In this study, we have assumed that the experimental
cavity is filled with water and has the following dimensions: h = 10 µm, L = 100 µm, and
the thickness is equal to 2 µm, as shown schematically in Figure 1.
R. Bashir mentioned [32] that DNA does in fact behave like a good heat conductor. It
was assumed that two complementary DNA strands could form a molecular switch that
operated between high and low resistance states. This is now regarded as a key ‘’device” in
molecular electronics [33–37].
Materials 2023, 16, 3334 5 of 14

If the DNA switch is irradiated with ultra-short (i.e., fs or as) laser pulses, the 1-D heat
equation, according to references [38–41], is as follows:

∂2 T v2 me ∂T 2Vv2 me T ∂2 T
2
+ + 2
− v2 2 = 0 (9)
∂t ћ ∂t ћ ∂x
where T is the temperature variation; me stands for the mass of the heat carriers in DNA,
which are actually electrons; X indicates the space coordinate; V represents the potential
carrier generated at the interface; t is the time, ν is the thermal wave velocity, and ћ is the
reduced Max-Planck constant.
Equation (9) derived by Kozlovski et al. [38,39] can be rewritten as:

∂2 T ∂T ∂2 T
+ ε + kT − α =0 (10)
∂t2 ∂t ∂X 2
where:
ν 2 me
ε≡ (11)
ћ

2Vν2 me
k≡ (12)
ћ2

α ≡ ν2 (13)
The source term, with respect to the boundary conditions, has been defined according
to Equations (1)–(8) and (14):
T ( x, y, z, ∞) = 0 (14)
According to Zhukovsky et al. [42], the solution of Equation (10) can be derived with
the help of the heat operator technique and is as follows:
Z ∞
εt t dξ t2 2 +4k)
T ( x, t) = e− 2 × √ 3 × e− 16ξ −ξ(ε × Ŝ f ( x ) (15)
4 π 0 ξ 2

Considering the heat operator Ŝ as:

2
Ŝ f ( x ) = e−4αξ∂x × f ( x ) (16)

where T is the temperature variation, t represents the time, ξ indicates the increment term,
Ŝ stands for the heat operator, and ε, k, and α are defined by Equations (11)–(13). In these
equations, f(x) is the source term, which is proportional to the incident power.
The aim was to derive an analytical formula for the most general case of an incident
laser beam, given the solution to a term describing the source of the form xm . This is
due to the linear superposition properties of the heat equation solutions. Considering the
equations presented in Ref. [42], the general form (for the source term: xm ) is given by:
tε
te− 2 +γ×( x) ∞
Z 
du t2 −nδ
− 16u
T ( x, t) = √ × ×e ×Hm ( x, 0) (17)
4 π 0 u3/2

where:  
δ = ε2 + 4 K + αγ2 (18)

Here Hm ( x, 0) is the m-kind Hermite polynomial with two variables, when y = 0. For
example (m ∈ {1, 2, 3, 4, 5}) :
H20 ( x, 0) = 1 (19)

H21 ( x, 0) = 2x (20)
Materials 2023, 16, 3334 6 of 14

H22 ( x, 0) = 4x2 − 2 (21)

H23 ( x, 0) = 8x3 − 12x (22)

H24 ( x, 0) = 16x4 − 48x2 − 12 (23)

H25 ( x, 0) = 32x5 − 160x3 − 120x (24)

3. Simulations
The interaction between the laser beam and two strands of DNA was simulated using
the “MATHEMATICA” software 11. The main input data are compiled in Table 1 [39].
It is further assumed that the incident laser power was of p = 1 W and the beam waist
was w = 50 µm. A Core i7, 8th generation computer with 32 GB of RAM was used for the
calculations. Computation times were generally less than 20 s.

Table 1. Input data used in the MATHEMATICA software 11 [39].

Item Value Unit

Thermal wave velocity (υ) 0.05 nm fs−1
Characteristic temperature at the molecular level 316 K
Pulse duration 100 fs
Potential 3.25 × 10−3 eV

It is estimated that the HAZ, in this case, is (χτ)0.5 . In this simulation, χ = 0.143 m2 s−1
was estimated based on the assumption that it is the same as in the case of water at 25 ◦ C
and τ = 10–13 s, due to the fact that more than 73% of the human soft man body tissue
is composed of water [40]. The model simulation therefore assumes that the thermal
parameters of the tissue are identical to those of water.
This gives the result HAZ = 0.13 µm, which is no more than 2.6 × 10−3 (%) with respect
to the beam radius of 25 µm. Therefore, our estimates of the temperature distribution under
laser irradiation are highly accurate.
It should be noted that for ns laser pulses, the HAZ increases significantly to 75 µm or
more. This significantly reduces the time and space accuracy of the simulations.

4. Results and Discussion

Figures 2a, 3a and 4a show the functions H[1,y], H[2,y], and H[4,y] respectively. These
functions are very important in the final solution of the heat equation. 3D, 2D, and 1D
thermal fields versus x and irradiation time, t, are displayed in Figures 2–4 (b), (c), and (d),
respectively. In fact, the X-axis is the only one where the laser beam asymmetry can
manifest, while along the Z-axis one has constant or close to zero values for the laser
intensity variation of the strand junction of DNA. It should also be noted that for a very
small y, the Hermite function becomes either very close to zero (for n—odd) or constant
(for n—even). Note that T in the model equations is actually dT in Figures 2–4. Comparing
Figure 2 with Figures 3 and 4, it can be concluded that the thermal fields generated by type
H[1,y] (n-odd) are suitable for laser stretching of DNA, and those of H[2,y] and H[4,y]
are excellent for cancer treatment. The thermal fields generated in the cases of H[2,y] and
H[4,y] (n-even) are very close to Bragg peaks, so in the case of certain tissue surfaces, it is
preferable to replace the laser irradiation with particles such as electrons, protons, or ions.
Materials 2023,16,
Materials2023, 16,3334
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7 of 1514

Figure 2.
Figure 2. Analytical
Analytical simulations
simulationsusing
using“MATHEMATICA”
“MATHEMATICA”software
software11:
11:(a)
(a)Hermite
Hermite(1,(1,y)y)plot;
plot;
(b)(b)
3D
3D plot; (c) 2D plot; and (d) 1D plot; using the following input parameters: T fields (a,b) in DNA
plot; (c) 2D plot; and (d) 1D plot; using the following input parameters: T fields (a,b) in DNA with a
with a power of p = 1 W and a laser irradiation time of t = 100 fs. Here, y and z ≈ 0.
power of p = 1 W and a laser irradiation time of t = 100 fs. Here, y and z ≈ 0.

Figures 2a, 3a and 4a present the graphs of H[1,y], H[2,y], and H[4,y] respectively.
Numerous simulations of such functions show that for n-odd, all the graphs are well
described by the functions close to zero along the y-axis, such as H[1,y]. On the other
hand, the functions such as H[2,y] and H[4,y] are constants, and this is true for all the
n-even. The above observations are made within the limits of computer performances and
MATHEMATICA software 11 packages.
Materials 2023,16,
Materials2023, 16,3334
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Figure 3. Analytical simulations using “MATHEMATICA” software 11: (a) 3D plot and (b) 2D plot
Figure 3. Analytical simulations using “MATHEMATICA” software 11: (a) 3D plot and (b) 2D plot
for a laser irradiation time of t = 500 fs; (c) 3D plot and (d) 2D plot for a laser irradiation time of t =
for
1000a fs.
laser
Theirradiation
following time
inputofparameters
t = 500 fs;were
(c) 3D plot and
applied: (d) 2D(a,b)
T fields plotinfor
DNAa laser
withirradiation
a power oftime
p = 1of
tW;
= 1000 fs. The
y and z ≈ 0. following input parameters were applied: T fields (a,b) in DNA with a power of
p = 1 W; y and z ≈ 0.

These observations are very important because it is only along the x-axis that the laser
beam produces significant variations in the thermal fields. On the z-axis the situation is the
same as on the y-axis, since the z variation is close to zero and therefore the temperature
variation (absorption coefficient) is also very small (close to that of water).
Figure 3 shows analytical simulations in which all the parameters used in Figure 2 are
unchanged, except for the irradiation time, which is 5 to 10 times longer than that used in
the simulation in Figure 2. However, the comparison of the 3D and 2D plots from borg
Figures 2 and 3 shows that the temperatures behave non-linearly as the irradiation time is
varied due to the quantum effect of the modified heat equation described in Equation (9).
Materials 2023,16,
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Figure 4. Analytical simulations using “MATHEMATICA” software 11: (a) 3D plot and (b) 2D plot
Figure 4. Analytical simulations using “MATHEMATICA” software 11: (a) 3D plot and (b) 2D plot
for a laser incident power of 0.2 W; (c) 3D plot and (d) 2D plot for a laser incident power of 0.1 W.
for a laser incident power of 0.2 W; (c) 3D plot and (d) 2D plot for a laser incident power of 0.1 W.
The following input parameters were applied: T fields (a,b) in DNA with a laser irradiation time of
The following
t = 100 fs; y andinput
z ≈ 0.parameters were applied: T fields (a,b) in DNA with a laser irradiation time of
t = 100 fs; y and z ≈ 0.
Figures 2a–4a present the graphs of H[1,y], H[2,y], and H[4,y] respectively.
The simulations
Numerous simulations performed with different
of such functions showlaser
thatpowers showalla the
for n-odd, direct proportionality
graphs are well
between
described by the functions close to zero along the y-axis, such as H[1,y]. DNA
the incident laser power and the temperature variation of the target On themolecule,
other
with
hand, the functions such as H[2,y] and H[4,y] are constants, and this is true for behavior
the same plot shapes and corresponding proportional values (Figure 4). This all the
is induced
n-even. Thebyabove
Equation (7), whichare
observations represents
made withinthe solution
the limits of the heat equation.
of computer However,
performances
this model also has limitations
and MATHEMATICA software 11 packages. induced by the heating laser intensity, which at values
higher than 1 W leads to DNA degradation, making the model inapplicable.
These observations are very important because it is only along the x-axis that the
The
laser beam simulations
produces shown in Figures
significant 2a, 5a
variations inand
the 6a, the Hermite
thermal fields. Onplots,
thedesignate
z-axis thethe
theoretical input data for the present simulation based on the laser intensity.
situation is the same as on the y-axis, since the z variation is close to zero and therefore The main
graphs, Figures 2b,variation
the temperature 3a,c and (absorption
4a,c, as wellcoefficient)
as Figures 5bis and
also6b, present
very smallthe 3D distributions
(close to that of
of the
water).thermal field as a function of space and time. It can be seen that for n-odd (Figure 2b),
we have a temperature variation that is very suitable to use in DNA
Figure 3 shows analytical simulations in which all the parameters used in Figure elongation without
2 are
destroying
unchanged, except for the irradiation time, which is 5 to 10 times longer than that used The
the information contained in the DNA, which is fitting for its analysis. in
thermal fields in the case of n-even are very high as variations for graphs close to x = 0,
Materials 2023, 16, 3334 10 of 14

which is exactly the opposite situation compared to n-odd. On the other hand, if the laser
intensity is increased slightly, the DNA information can be destroyed without causing very
much damage to the living cells around the diseased cell. Future research in this field may
take advantage of the fact that, in this situation, the thermal field is close to that of the Bragg
peaks produced by irradiation with electrons, protons, and ions. The shapes of the graphs
in Figures 2c, 3b,d, 4b,d, 5c and 6c depict the 2D density plot at the same temperature
distribution. Figures 2d, 5d and 6d are variants of a 2D and 1D figure, showing the thermal
field at a given time. Again, these graphics are limited by computer performance and
Materials 2023, 16, x FOR PEER REVIEW 11 of 15
software capabilities. It is noted that the 1D, 2D, and 3D thermal field distributions are in
good agreement with experimental data from the literature [23].

Figure 5. Analytical simulations using “MATHEMATICA” software 11: (a) Hermite (2, y) plot; (b)
Figure 5. Analytical simulations using “MATHEMATICA” software 11: (a) Hermite (2, y) plot; (b) 3D
3D plot; (c) 2D plot; and (d) 1D plot, using the following input parameters: T-fields (a–d) in DNA
plot;
with (c) 2D plot;
a power of pand
= 1(d) 1D plot,
W and using
a laser the following
irradiation time ofinput parameters:
t = 100 fs. Here, yT-fields
and z ≈ (a–d)
0. in DNA with a
power of p = 1 W and a laser irradiation time of t = 100 fs. Here, y and z ≈ 0.
Materials 2023, 16, 3334 11 of 14
Materials 2023, 16, x FOR PEER REVIEW 12 of 15

Figure 6. Analytical simulations using “MATHEMATICA” software 11: (a) Hermite (4, y) plot; (b)
Figure 6. Analytical simulations using “MATHEMATICA” software 11: (a) Hermite (4, y) plot; (b) 3D
3D plot; (c) 2D plot; and (d) 1D plot, using the following input parameters: T fields (a,b) in DNA
plot;
with (c) 2D plot;
a power of pand
= 1 (d) 1D plot,
W and using
a laser the following
irradiation time ofinput parameters:
t = 100 T fields
fs. Here, y and (a,b) in DNA with a
z ≈ 0.
power of p = 1 W and a laser irradiation time of t = 100 fs. Here, y and z ≈ 0.
Since the analytical simulations using the Hermite (3, y) plot have the same shape as
Since the analytical
the simulation simulations
in Figure 2, these wereusing the Hermite
not presented (3,paper.
in the y) plot have the same shape as
the simulation in Figure 2, these were not presented in the paper.
5. Conclusions
5. Conclusions
A new generalized model based on the quantum heat transport equation is
A new generalized model based on the quantum heat transport equation is proposed
proposed to describe the interaction of ultra-short (fs) asymmetric moderate intensity
to describe the interaction of ultra-short (fs) asymmetric moderate intensity laser beams
laser beams with anisotropic DNA, in order to come closer to the actual experimental
with anisotropic DNA, in order to come closer to the actual experimental research. A highly
research. A highly accurate formula was derived to describe the temperature field in
accurate formula was derived to describe the temperature field in DNA samples during
DNA samples during laser irradiation. The thermal distribution generated in the
laser irradiation. The thermal distribution generated in the irradiated DNA strands was
irradiated DNA strands was introduced by splitting the laser beam into transverse
introduced by splitting the laser beam into transverse Hermite-Gauss modes. Fluctuations
Hermite-Gauss modes. Fluctuations in laser intensity were accounted for by modeling
in laser intensity were accounted for by modeling them as superpositions of Hermite-Gauss
them as superpositions of Hermite-Gauss laser modes.
laser modes.
It was demonstrated that only source terms of the form a 𝑥 do not exhibit
circular symmetry, which proves to be an efficient computational model for molecular
electronics simulations.
Materials 2023, 16, 3334 12 of 14

It was demonstrated that only source terms of the form am x m do not exhibit cir-
cular symmetry, which proves to be an efficient computational model for molecular
electronics simulations.
The new model can be rather easily extended to other ultra-short laser pulses or
to interactions with substances of biological interest. This makes it easy to predict the
important temperature variation due to fluctuations in the power of the incident laser
beams. It should be noted that the previous version of these analyses [40] proved to be
incapable of calculating the temperature field variation due to laser intensity fluctuations
present in real experiments [43].
Precise values for the temperature field are required because DNA testing must be
carried out without destroying the target information, and cancer treatment must locally
destroy the affected DNA strands. It is important to note that, according to this study, the
temperature variations do not exceed 10 K so that the DNA information can be preserved.
The simulations carried out with different laser powers show a direct proportional-
ity between the laser power and the temperature variation of the target DNA molecule,
presenting the same plot shapes and corresponding proportional values. However, as the
irradiation time varies, the temperatures behave in a non-linear manner.
However, the model is also limited by the intensity of the laser beam because, at high
intensities, the DNA breaks down and the model becomes inapplicable. In conclusion, the
present paper deals with molecular electronics, presenting a new model that mixes the
Kozlowski physical model with Zhukovsky’s recent radical approach to solving equations
with partial derivates. This model is simplified and does not take into account the DNA’s
internal structure. The proposed model has a fast simulation time of less than 1 min, which
can be easily achieved on inexpensive commercial PCs. This avoids the need for complex
and time-consuming software simulations such as molecular dynamics simulations [20].
We also suggest a replacement of electron, proton, and ion beam sources used in cancer
treatment with laser beams.

Author Contributions: M.O., C.N.M. and A.M.I.T. contributed in equal proportions in the present
paper. Conceptualization, M.O.; methodology, M.O., C.N.M. and A.M.I.T.; software, M.O. and
C.N.M.; validation, M.O., C.N.M. and A.M.I.T.; formal analysis, M.O.; investigation, M.O., C.N.M.
and A.M.I.T.; resources, M.O., C.N.M. and A.M.I.T.; data curation, M.O., C.N.M. and A.M.I.T.;
writing—original draft preparation, M.O. and A.M.I.T.; writing—review and editing, A.M.I.T.; visu-
alization, M.O., C.N.M. and A.M.I.T.; supervision, M.O., C.N.M. and A.M.I.T.; project administration,
M.O., C.N.M. and A.M.I.T.; funding acquisition, M.O. and C.N.M. All authors have read and agreed
to the published version of the manuscript.
Funding: This research was supported by the Romanian Ministry of Research, Innovation, and
Digitalization under the Romanian National Nucleu Program LAPLAS VII—contract no. 30N/2023.
Institutional Review Board Statement: Not applicable.
Informed Consent Statement: Not applicable.
Data Availability Statement: The data presented in this study are available on request from the
corresponding authors.
Acknowledgments: The authors would like to thank Ion N. Mihailescu for his scientific and
technical support.
Conflicts of Interest: The authors declare no conflict of interest.

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