George Kalosakas

University of Patras | UP · Department of Material Science

Relative lifetimes of inherent double stranded DNA openings with lengths up to ten base pairs are presented for different gene promoters and corresponding mutants that either increase or decrease transcriptional activity in the framework of the Peyrard–Bishop–Dauxois model. Extensive microcanonical simulations are used with energies corresponding t...

Relative lifetimes of inherent double stranded DNA openings with lengths up to ten base pairs are presented for different gene promoters and corresponding mutants that either increase or decrease transcriptional activity, in the framework of the Peyrard-Bishop-Dauxois model. Extensive microcanonical simulations are used, with energies corresponding...

We investigate the distribution of bubble lifetimes and bubble lengths in DNA at physiological temperature, by performing extensive molecular dynamics simulations with the Peyrard-Bishop-Dauxois (PBD) model, as well as an extended version (ePBD) having a sequence-dependent stacking interaction, emphasizing the effect of the sequences' guanine-cytos...

We study the chaotic dynamics of graphene structures, considering both a periodic, defect free, graphene sheet and graphene nanoribbons (GNRs) of various widths. By numerically calculating the maximum Lyapunov exponent, we quantify the chaoticity for a spectrum of energies in both systems. We find that for all cases, the chaotic strength increases...

Thermal transport in nanostructured transition metal dichalcogenides has been examined using molecular dynamics simulations. The study is focused on the calculation of the thermal conductivities of pristine and periodically patterned MX2 crystals, assessing the effects of patterning these materials with stripes of substitutional defects. The influe...

Abstract: Using molecular dynamics with semi-empirical potentials the phonon spectra of MoS2 were examined under tensile stress.

We discuss the effect of heterogeneity on the chaotic properties of the Peyrard-Bishop-Dauxois nonlinear model of DNA. Results are presented for the maximum Lyapunov exponent and the deviation vector distribution. Different compositions of adenine-thymine (AT) and guanine-cytosine (GC) base pairs are examined for various energies up to the melting...

We examine the mechanical response of single layer graphene nanoribbons (GNR) under constant compressive loads through molecular dynamics simulations. Compressive stress-strain curves are presented for GNRs of various lengths and widths. The dependence of GNR's buckling resistance on its size, aspect ratio, and chiral angle is discussed and approxi...

The mechanical response of single and multiple graphene sheets under uniaxial compressive loads was studied with molecular dynamics simulations, using different semi-empirical force fields at different boundary conditions or constrains. Compressive stress-strain curves were obtained and the critical stress/strain values were derived. For single lay...

We consider a drug release formulation and investigate the evolution of the fraction of drug molecules that are sufficiently close to the release boundary, in order to check the validity of the assumption underlying the theoretical derivation of a stretched exponential (Weibull) release kinetics. Diffusion-controlled drug release from spheres and s...

The mechanical response of single and multiple graphene sheets under uniaxial compressive loads was studied with molecular dynamics (MD) simulations, using different semi-empirical force fields at different boundary conditions or constrains. Compressive stress-strain curves were obtained and the critical stress/strain values were derived. TheMDresu...

Thin membranes, such as monolayer graphene of monoatomic thickness, are bound to exhibit lateral buckling under uniaxial tensile loading that impairs its mechanical behaviour. In this work, we have developed an experimental device to subject 2D materials to controlled equibiaxial strain on supported beams that can be flexed up or down to subject th...

We discuss diffusion-controlled drug release from slabs or thin films. Analytical and numerical results are presented for slabs with flat surfaces, having a uniform thickness. Then, considering slabs with rough surfaces, the influence of inhomogeneous slab thickness on release kinetics is numerically investigated. The numerical release profiles are...

A method that utilises atomic trajectories and velocities from molecular dynamics simulations has been suitably adapted and employed for the implicit calculation of the phonon dispersion curves of graphene. Classical potentials widely used in the literature were employed. Their performance was assessed for each individual phonon branch and the over...

We numerically demonstrate the spontaneous formation of various 3D carbon nanostructures, like multi-tube carbon nanotubes, nanopyramids, nanocubes, artificially rippled graphene, and other exotic nanomaterials, starting from graphene nanoribbons and inducing controllably engineered defects consisting of carbon adatoms or inverse Stone-Wales defect...

We investigate, both analytically and numerically, diffusion-controlled drug release from composite spherical formulations consisting of an inner core and an outer shell of different drug diffusion coefficients. Theoretically derived analytical results are based on the exact solution of Fick's second law of diffusion for a composite sphere, while n...

Using molecular dynamics simulations with semi-empirical potentials, we demonstrate a method to fabricate carbon nanotubes (CNTs) from graphene nanoribbons (GNRs), by periodically inserting appropriate structural defects into the GNR crystal structure. We have found that various defect types initiate the bending of GNRs and eventually lead to the f...

Relative reaction rates for hole transfer between G radical cations and GGG triplets in DNA, through different bridges of varying lengths, are numerically calculated and the obtained results are compared with corresponding experimental observations [Giese et al., 2001, Nature, 412, 318; Angew. Chem., Int. Ed., 1999, 38, 996]. Hole donors and accept...

The pressure evolution of the Raman spectrum of graphene grown by chemical vapour deposition on polycrystalline copper is investigated with the use of a polar and a non-polar pressure transmitting medium (PTM). The G and 2D Raman bands exhibit similar pressure slopes for both PTM irrespectively of any unintentional initial doping and/or strain of t...

Bond stretching and angle bending force fields, appropriate to describe in-plane motion of graphene sheets, are derived using first principles' methods. The obtained force fields are fitted by analytical anharmonic energy potential functions, providing efficient means of calculations in molecular mechanics simulations. Numerical results regarding t...

We numerically calculate drug release profiles from simple spherical devices using Monte Carlo simulations, when diffusion is the dominant release mechanism. Release curves are accurately described by the stretched exponential function, also known as the Weibull function. The dependence of the two stretched exponential parameters on the size of the...

Using ab initio and molecular dynamics simulations with semi-empirical potentials, the phonon density of states (PnDOS) of graphene with different types of defects such as substitution atoms (Si), carbon isotopes (12C and 14C), and vacancies was calculated. The main interest was to investigate the possibility to generate phononic band gaps (PBGs) i...

The diffusion coefficient is calculated for a charge propagating along a double-stranded DNA, while it interacts with the nonlinear fluctuational openings of base pairs. The latter structural dynamics of DNA is described by the Peyrard-Bishop-Dauxois model [T. Dauxois, M. Peyrard, and A. R. Bishop, Phys Rev. E 47 R44 (1993)], which represents essen...

We mapped promoter regions of double-stranded DNA with respect to the probabilities of appearance of relatively large bubble openings exclusively due to thermal fluctuations at physiological temperatures. We analyzed five well-studied promoter regions of procaryotic type and found a spatial correlation between the binding sites of transcription fac...

We systematically examine all the tight-binding parameters pertinent to charge transfer along DNA. The pi molecular structure of the four DNA bases (adenine, thymine, cytosine, and guanine) is investigated by using the linear combination of atomic orbitals method with a recently introduced parametrization. The HOMO and LUMO wave functions and energ...

The pi�-pi�* molecular structure (eigenenergies and eigenfunctions) of flavin tricyclic ring is calculated, using the linear combination of atomic orbitals (LCAO) method containing only pz atomic orbitals. In respect to FADH− position opposite to DNA lesion in photolyase, flavin’s HOMO is found to be distributed in the central and distal side, whil...

A novel parametrization within a simplified LCAO model (a type of Hückel model) is presented for the description of π molecular orbitals in organic molecules containing π-bonds between carbon, nitrogen, or oxygen atoms with sp2 hybridization. It is shown that the model is quite accurate in predicting the energy of the highest occupied π orbital and...

We systematically examine all the tight-binding parameters pertinent to charge transfer along DNA. The $\pi$ molecular structure of the four DNA bases (adenine, thymine, cytosine, and guanine) is investigated by using the linear combination of atomic orbitals method with a recently introduced parametrization. The HOMO and LUMO wavefunctions and ene...

We present numerical results on the temperature dependence of the distribution of bubble lengths in DNA segments of various guanine-cytosine (GC) concentrations. Base-pair openings are described by the Peyrard-Bishop-Dauxois model and the corresponding thermal equilibrium distributions of bubbles are obtained through Monte Carlo calculations for bu...

We present numerical results on the temperature dependence of the distribution of bubble lengths in DNA segments of various guanine-cytosine (GC) concentrations. Base-pair openings are described by the Peyrard-Bishop-Dauxois model and the corresponding thermal equilibrium distributions of bubbles are obtained through Monte Carlo calculations for bu...

The distribution of bubble lengths in double-stranded DNA is presented for segments of varying guanine-cytosine (GC) content, obtained with Monte Carlo simulations using the Peyrard-Bishop-Dauxois model at 310 K. An analytical description of the obtained distribution in the whole regime investigated, i.e., up to bubble widths of the order of tens o...

We report non-exponential decay of the time-dependent autocorrelation functions of base-pair opening dynamics in a model of DNA. Complex fluctuations occur in a wide temperature range, extending from below 200K up to the premelting transition regime above physiological temperatures. At least two distinct decay processes at different time scales are...

Comment on T.S. van Erp, S. Cuesta-Lopez, J.-G. Hagmann, and M. Peyrard, Phys. Rev. Lett. 95, 218104 (2005) [arXiv: physics/0508094].

In-plane, inter-carrier correlations in hole doped cuprates are investigated by ab initio multiconfiguration calculations. The dressed carriers display features that are reminiscent of both Zhang-Rice (ZR) CuO4 singlet states and Jahn-Teller polarons. The interaction between these quasiparticles is repulsive. At doping levels that are high enough,...

We study a dimer system of a generalized discrete nonlinear Schrödinger equation that interpolates between the integrable Ablowitz-Ladic equation and the nonintegrable discrete nonlinear Schrödinger equation (DNLS). We find analytically and verify numerically the occurrence of selftrapping in the parameter space of the two nonlinearity coefficients...

Multi-peaked localized stationary solutions of the discrete nonlinear Schrodinger (DNLS) equation are presented in one (1D) and two (2D) dimensions. These are excited states of the discrete spectrum and correspond to multi-breather solutions. A simple, very fast, and efficient numerical method, suggested by Aubry, has been used for their calculatio...

Comment on T.S. van Erp, S. Cuesta-Lopez, J.-G. Hagmann, and M. Peyrard, Phys. Rev. Lett. 95, 218104 (2005) [arXiv: physics/0508094].

We present the ac response of a DNA charge transport model, where the charge in the pi-stack interacts with the base-pair opening dynamics of the double strand. The calculated ac conductivity exhibits prominent peaks at polaron normal modes with electronic character, while weaker response appears at lower frequencies in the vibrational part of the...

We present results on the diffusive motion of a charge interacting with the nonlinear dynamics of a thermalized underlying lattice. Signatures of anomalous diffusive properties are found at relatively high temperatures, where highly nonlinear excitations are present. A sublinear diffusion and a plateau appear before the standard long-time diffusion...

The semi-classical Holstein model is used to account for experimental observations of electron dynamics in two-dimensional systems and assign transient spectral features formerly attributed to formation of small polarons. Our results show that the intraband relaxation of initial Bloch states is not directly followed by formation of the ground-state...

We report successful comparisons between model predictions for intrinsic thermal openings and experimental transcription data, showing that large and slow thermally induced openings (bubbles) of double-stranded DNA coincide with the location of start sites for transcription. Investigating viral and bacteriophage DNA gene promoter segments, we find...

We consider a minimal coupled charge / excitation-lattice model capturing a competition between linear polaronic self-trapping and the self-focusing effects of a soft nonlinear on-site potential. The standard single-humped polaron ceases to exist above a critical value of the coupling strength, closely related to the inflection point in the nonline...

We compare numerical calculations and experimental data showing that large, slow thermally-induced openings of double stranded DNA coincide with the location of functionally relevant sites for transcription. Investigating a bacteriophage DNA gene promoter segment, we find that the large opening tends to occur at the transcription start site. Other...

We report numerical simulations of the contribution of the transverse hydrogen bond stretching vibrations in the dynamic structure factor of a DNA sequence. We apply a simple nonlinear dynamical model to a finite segment of the bacteriophage T7 core promoter DNA. The temperature dependence of the dynamic structure factor is investigated. A distinct...

We discuss temperature effects in a model of charge transport in DNA. The charge is coupled to the lattice distortions and therefore temperature induced fluctuations and coherent base-pair openings (“bubbles”) directly affect the charge’s motion. The influence of the charge–lattice coupling constant on polaronic behavior, as well as the effect of d...

Thermally-induced openings of double stranded DNA were studied, by using a microscopic nonlinear dynamical model. Our results show that the larger fluctuating bubbles coincide with the location of functionally relevant sites for transcription; at the transcription start site and other regulatory sites. Both viral and bacteriofagus DNA gene promoter...

It has long been known that double‐stranded DNA is subject to temporary, localized openings of its two strands. Particular regions along a DNA polymer are destabilized structurally by available thermal energy in the system. The localized sequence of DNA determines the physical properties of a stretch of DNA, and that in turn determines the opening...

A number of experimental and theoretical works have suggested the relevance of polaronic effects for charge migration in DNA. We have previously introduced the Peyrard-Bishop-Holstein model as an appropriate model for the description of such effects. The polaron normal modes are expected to manifest themselves through the response of the system in...

Presence of strong nonlinearity in a material, either explicit, or effective (resulting from the interaction of coupled degrees of freedom), can lead to intrinsic inhomogeneity even in a periodic extended system. We briefly discuss two examples where such a breaking of the translational symmetry due to nonlinearity (i) determines the optical featur...

We present analytical relations for the quantum evolution of the number difference of bosons between the two sites of a double-well potential, by using perturbative results for small tunneling amplitudes in the two-mode approximation. Results are obtained for two different initial conditions: completely localized states and coherent spin states. In...

The full quantum dynamics of many bosons that are initially completely localized on one site of a symmetric dimer is investigated in the small tunnelling amplitude regime. The number difference of bosons between the two equivalent sites of the dimer exhibits rich behaviour on different timescales, ranging from small amplitude oscillations and colla...

Following a short introduction on localized modes in a model system, namely the discrete nonlinear Schrodinger equation, we present explicit results pertaining to three different physical systems described by similar equations. The applications range from the Raman scattering spectra of a complex electronic material through intrinsic localized vibr...

We calculate the opening probabilities along specific DNA viral sequences used in experimental transcription studies. A nonlinear dynamical model for the base-pair openings is able to account for the details of the openings need to initiate transcription. The obtained results for different viruses and for a few mutations are in a very good correlat...

We study temperature effects on the characteristic time for which charge carriers remain spatially confined while interacting with fluctuational openings (bubbles) of double stranded DNA. Using semiclassical molecular-dynamics simulations, we find that in the low-temperature regime this characteristic time decreases in a power-law fashion with temp...

An effective nonlinear model has been recently proposed to account for the overtone Raman redshifts of isotopically pure Pt35Cl and Pt37Cl [N. K. Voulgarakis et al., Phys. Rev. B 64, 020301(R) (2001)]. Using values of the parameters of the model that are consistent with independent calculations from the phonon dispersion and from the underlying ele...

A Bose-Einstein condensate trapped in a two-dimensional optical lattice exhibits an abrupt transition manifested by the macroscopic wave function changing character from spatially localized to extended. Resulting from a bifurcation, this irreversible transition takes place as the interwell potential barrier is adiabatically decreased below a critic...

The most direct experimental indication of microscopic vibrational intrinsic localized modes in a bulk material is provided by the resonance Raman spectra of both naturally abundant and isotopically pure PtCl. PtCl is the strong charge density wave compound [Pt(en)_2][Pt(en)_2Cl_2](ClO_4)_4, where en=ethylenediamine. An effective nonlinear model ha...

We investigate propagation of a charge carrier along intrinsically dynamically disordered double-stranded DNA. This is realized by the semiclassical coupling of the charge with a nonlinear lattice model that can accurately describe the statistical mechanics of the large amplitude fluctuations of the base pairs leading to the thermal denaturation tr...

We present an improved algorithm of the self-consistent mean-field implementation that has been recently proposed for the calculation of block copolymer self-assembly. Without requiring prior knowledge of the symmetry of the mesophase segregation, the algorithm is numerically stable and significantly faster than previously proposed methods. These a...

Analytical expressions for the energy eigenstates of the boson-Hubbard (or quantum discrete-nonlinear Schrödinger) dimer are obtained by applying perturbation theory in the small-tunneling-amplitude limit. The results are relevant for a Bose-Einstein condensate trapped in a double-well potential. A detailed comparison with the numerical solutions a...

Monte Carlo simulations and mean-field models are used for the study of nonequilibrium reactions taking place on the surface of a catalyst. The model represents the catalytic reduction of NO with H2 on a Pt surface. Both Monte Carlo simulations and mean-field results predict the existence of a critical surface in the parameter space where the catal...

We study the many-quanta problem of an intramolecular vibrational excitation interacting with optical phonons, that may represent the nonlinearity from intrinsic electron-lattice interactions. In the adiabatic limit we calculate numerically the ground-state energy and the corresponding wave functions for N vibrational quanta. In the one-dimensional...

We study the many quanta problem of an intramolecular vibrational excitation interacting with optical phonons. In the adiabatic limit we calculate numerically the ground state for N vibrational quanta. We find strong red-shifts in the overtone spectra and an increasing spatial localization as the number of quanta increases. Through model parameter...

We present a system of coupled degrees of freedom that can effectively describe the localization of intra-molecular excitations in the charge transfer solid PtCl. These excitations correspond to the Raman active motion of chlorines (symmetric Pt - Cl stretching). By fitting two parameters of the model we obtain an accurate description of the strong...

We study the properties of a modified discrete non-linear Schrodinger equation (MDNLS) that arises from the coupling of an excitation to an acoustic chain. We find exact results for self-trapping in chains of two and three sites and approximate results for longer chains. We also study possible recurrence phenomena in the equation and compare our fi...

We use a stationary and normal mode analysis of the semiclassical Holstein model in order to connect the low-frequency linear polaron modes to low-lying far-infrared lines of the acetanilide spectrum and through parameter fitting we comment on the validity of the polaron results in this system.

We investigate polaron properties in the semiclassical Holstein model in one, two, and three dimensions, using two methods: a simple and efficient numerical scheme and a variational approach. We obtain accurate information on the energy and the existence regimes of the polaron state. We study small oscillations of the polaron through normal-mode an...

The existence of time-periodic localized solutions near the anticontinuous limit in a generalized Holstein model with anharmonic on-site oscillators has been rigorously proved [S. Aubry, Physica D 103 (1997) 201]. In the present work we calculate explicitly such solutions, called polarobreathers, starting from the anticontinuous limit with the use...

In the context of the soliton mechanism for proton transport in hydrogen-bonded networks we analyze properties of kink propagation through disordered hydrogen-bonded chain when realistic mass variation along the chain is created through deuterium substitutions. We provide an interpretation for the kink propagation in the chain as the motion of a pa...

We present temperature effects on the characteristic time at which charge carriers remain spatially confined while interacting with fluctuational openings of DNA. Using semiclassical molecular dynamics simulations, we find that in the low temperature regime this characteristic time decreases in a power-law fashion with temperature and coincides wit...

A Bose-Einstein condensate trapped in a two-dimensional optical lattice exhibits an abrupt transition manifested by the macroscopic wavefunction changing character from spatially localized to extended. This transition takes place as the interwell potential barrier is adiabatically decreased below a critical value and is irreversible since increasin...

We calculate numerically the polaron state and its energy for the two-dimensional adiabatic Holstein model. We find two critical values of the coupling parameter χ. The maximum critical value χ c 2 determines the region where the polaron becomes unstable with respect to the extended Bloch states, and the other χ c 1 , determines the region where th...

Mελέτη των εντοπισμένων λύσεων του ημικλασικού προτύπου Holstein. Αριθμητική μέθοδος υπολογισμού των στάσιμων πολαρονικών λύσεων και ανα λυτικά αποτελέσματα με χρήση μεθόδου μεταβολών.Κανονικοί τρόποι ταλά ντωσης των πολαρονίων στα πλαίσια της προσέγγισης Born-Oppenheimer.Υπ ολογισμός των ιδιοταλαντώσεων του πλήρους προβλήματος με χρήση μετασχ ηματ...