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K. L. Sebastian

Publications and source records attributed to K. L. Sebastian.

18 recordsLinked to original sources

Diffusion caused by two noises-active and thermal

The diffusion of colloids inside an active system-e.g. within a living cell or the dynamics of active particles itself (e.g. self-propelled particles) can be modeled through overdamped Langevin equation which contains an additional noise term apart from the usual white Gaussian noise, originating from the thermal environment. The second noise is referred to as 'active noise' as it arises from activity such as chemical reactions. The probability distribution function (PDF or the propagator) in space-time along with moments provides essential information for understanding their dynamical behavior. Here we employ the phase-space path integral method to obtain the propagator, thereby moments and PDF for some possible models for such noise. At first, we discuss the diffusion of a free particle driven by active noise. We consider four different possible models for active noise, to capture the possible traits of such systems. We show that the PDF for systems driven by noises other than Gaussian noise largely deviates from normal distribution at short to intermediate time scales as a manifestation of out-of-equilibrium state, albeit converges to Gaussian distribution after a long time as a consequence of the central limit theorem. We extend our work to the case of a particle trapped in a harmonic potential and show that the system attains steady state at long time limit. Also, at short time scales, the nature of distribution is different for different noises, e.g. for particle driven by dichotomous noise, the probability is mostly concentrated near the boundaries whereas a long exponential tail is observed for a particle driven by Poissonian white noise.

cond-mat.stat-mech

Exact Results for the Tavis-Cummings and H$\boldsymbol{\ddot{u}}$ckel Hamiltonians with Diagonal Disorder

We present an exact method to calculate the electronic states of one electron Hamiltonians with diagonal disorder. We show that the disorder averaged one particle Green's function can be calculated directly, using a deterministic complex (non-Hermitian) Hamiltonian. For this, we assume that the molecular states have a Cauchy (Lorentz) distribution and use the supersymmetric method which has already been used in problems of solid state physics. Using the method we find exact solutions to the states of $N$ molecules, confined to a microcavity, for any value of $N$. Our analysis shows that the width of the polaritonic states as a function of $N$ depend on the nature of disorder, and hence can be used to probe the way molecular energy levels are distributed. We also show how one can find exact results for H$\ddot{u}$ckel type Hamiltonians with on-site, Cauchy disorder and demonstrate its use.

quant-ph

Effects of disorder on polaritonic and dark states in a cavity using the disordered Tavis-Cummings model

We consider molecules confined to a microcavity whose dimensions are such that an excitation of the molecule is nearly resonant with a cavity mode. We investigate the situation where the excitation energies of the molecules are randomly distributed with a mean value of $ε_a$ and variance $σ$. For this case, we find a solution that approaches the exact result for large values of the number density $\mathscr{N}$ of the molecules. We find the conditions for the existence of the polaritonic states, as well as expressions for their energies. The polaritonic states are quite stable against disorder. Analytical results are verified by comparison with simulations. When $ε_a$ is equal to that of the cavity state $ε_c$ (on resonance) the gap between the two polaritonic states is found to increase with disorder, the increase being equal to $2 \frac{σ^2}{\sqrt{\mathscr{N}}|\tilde{V}|}$ where $\tilde{V}$ is the coupling of a molecular excitation to the cavity state. An analytic expression is found for the disorder induced width of the polaritonic peak. We results for various densities of states, and the absorption spectrum. The dark states that exist in the case $σ=0$ turn "grey" in presence of disorder with their contribution to the absorption increasing with $σ$. We analyze the effect of including lifetimes of the cavity and molecular states and find that in the strong coupling regime, the width of the polaritonic peaks is dominated by the lifetime effect and that disorder plays almost no role, if the Rabi splitting is sufficiently large. We also consider the case where there is (a) orientational disorder as well as (b) spatial variation of the cavity field and find that they effectively amount to a renormlisation of the coupling.

quant-ph

Unusual eigenvalue spectrum and relaxation in the Lévy Ornstein-Uhlenbeck process

We consider the rates of relaxation of a particle in a harmonic well, subject to Lévy noise characterized by its Lévy index $μ$. Using the propagator for this Lévy Ornstein-Uhlenbeck process (LOUP), we show that the eigenvalue spectrum of the associated Fokker-Planck operator has the form $(n+mμ)ν$ where $ν$ is the force constant characterizing the well, and $n,m\in\mathbb{N}$. If $μ$ is irrational, the eigenvalues are all non-degenerate, but rational $μ$ can lead to degeneracy. The maximum degeneracy is shown to be two. The left eigenfunctions of the fractional Fokker-Planck operator are very simple while the right eigenfunctions may be obtained from the lowest eigenfunction by a combination of two different step-up operators. Further, we find that the acceptable eigenfunctions should have the asymptotic behavior $|x|^{-n_1+n_2\;μ}$ as $|x| \rightarrow \infty$, with $n_1$ and $n_2$ being positive integers, though this condition alone is not enough to identify them uniquely. We also assert that the rates of relaxation of LOUP are determined by the eigenvalues of the associated fractional Fokker-Planck operator and do not depend on the initial state if the moments of the initial distribution are all finite. If the initial distribution has fat tails, for which the higher moments diverge, one would have non-spectral relaxation, as pointed out by Toenjes et. al (Physical Review Letters, 110, 150602 (2013)).

cond-mat.stat-mech

Analytical Treatment of Coherent Excitation Transfer in FMO Complex

We suggest a new method of studying coherence in finite level systems coupled to the environment and use it for the Hamiltonian that has been used to describe the light-harvesting pigment-protein complex. The method works with the adiabatic states and transforms the Hamiltonian to a form in which the terms responsible for decoherence and population relaxation are separated out. Decoherence is then accounted for non-perturbatively, and population relaxation using a Markovian master equation. Analytical results can be obtained for the seven level system and the calculations are very simple for systems with more levels. We apply the treatment to the seven level system and the results are in excellent agreement with the exact numerical results of Nalbach et al. (P. Nalbach, D. Braun, and M. Thorwart, Physical Review E, 84, 041926 (2011)). Our approach is able to account for decoherence and population relaxation separately. It is found that decoherence only causes damping of oscillations, and does not lead to transfer to the reaction centre. Population relaxation is necessary for efficient transfer to the reaction centre, in agreement with earlier findings. Our results show that the transformation to the adiabatic basis followed by a Redfield type of approach leads to results in good agreement with exact simulation.

quant-ph

Path Integral Formulation for Lévy Flights - Evaluation of the Propagator for Free, Linear and Harmonic Potentials in the Over- and Underdamped Limits

Lévy flights can be described using a Fokker-Planck equation which involves a fractional derivative operator in the position co-ordinate. Such an operator has its natural expression in the Fourier domain. Starting with this, we show that the solution of the equation can be written as a Hamiltonian path integral. Though this has been realized in the literature, the method has not found applications as the path integral appears difficult to evaluate. We show that a method in which one integrates over the position co-ordinates first, after which integration is performed over the momentum co-ordinates, can be used to evaluate several path integrals that are of interest. Using this, we evaluate the propagators for (a) free particle (b) particle subjected to a linear potential and (c) harmonic potential. In all the three cases, we have obtained results for both overdamped and underdamped cases.

cond-mat.stat-mech

Dynamics of pulled desorption with effects of excluded volume interaction: The p-Laplacian diffusion equation and its exact solution

We analyze the dynamics of desorption of a polymer molecule which is pulled at one of its ends with force $f$, trying to desorb it. We assume a monomer to desorb when the pulling force on it exceeds a critical value $f_{c}$. We formulate an equation for the average position of the $n^{th}$ monomer, which takes into account excluded volume interaction through the blob-picture of a polymer under external constraints. The approach leads to a diffusion equation with a $p$-Laplacian for the propagation of the stretching along the chain. This has to be solved subject to a moving boundary condition. Interestingly, within this approach, the problem can be solved exactly in the trumpet, stem-flower and stem regimes. In the trumpet regime, we get $τ=τ_{0}n_d^{2}$ where $n_d$ is the number of monomers that have desorbed at the time $τ$. $τ_{0}$ is known only numerically, but for $f$ close to $f_{c}$, it is found to be $τ_{0}\sim f_c/(f^{2/3}-f_{c}^{2/3})$. If one used simple Rouse dynamics, this result changes to {\normalsize $τ\sim f_c n_d^2/(f-f_{c})$.} In the other regimes too, one can find exact solution, and interestingly, in all regimes $τ\sim n_d^2$.

cond-mat.soft

Conductance of a photochromic molecular switch with graphene leads

We report a full self-consistent ab initio calculation of the conductance of a diarylethene-based molecular switch with two graphene electrodes. Our result show the contributions of the resonant states of the molecule, of the electrode density of states, and of graphene unique features such as edge states. The conductivities are found to be significantly different for the two photochromic isomers at zero and finite applied bias. Further we point out the possibility of causing the switching by the application of a large potential difference between the two electrodes.

cond-mat.mes-hall

The dynamics of loop formation in a semiflexible polymer

The dynamics of loop formation by linear polymer chains has been a topic of several theoretical/experimental studies. Formation of loops and their opening are key processes in many important biological processes. Loop formation in flexible chains has been extensively studied by many groups. However, in the more realistic case of semiflexible polymers, not much results are available. In a recent study (K. P. Santo and K. L. Sebastian, Phys. Rev. E, \textbf{73}, 031293 (2006)), we investigated opening dynamics of semiflexible loops in the short chain limit and presented results for opening rates as a function of the length of the chain. We presented an approximate model for a semiflexible polymer in the rod limit, based on a semiclassical expansion of the bending energy of the chain. The model provided an easy way to describe the dynamics. In this paper, using this model, we investigate the reverse process, i.e., the loop formation dynamics of a semiflexible polymer chain by describing the process as a diffusion-controlled reaction. We perform a detailed multidimensional analysis of the problem and calculate closing times for a semiflexible chain which leads to results that are physically expected. Such a multidimensional analysis leading to these results does not seem to exist in the literature so far.

cond-mat.soft

Diffusion of Macromolecules across the Nuclear Pore Complex

Nuclear pore complexes (NPCs) are very selective filters that monitor the transport between the cytoplasm and the nucleoplasm. Two models have been suggested for the plug of the NPC. They are (i) it is a reversible hydrogel or (ii) it is a polymer brush. We propose a mesoscopic model for the transport of a protein through the plug, that is general enough to cover both. The protein stretches the plug and creates a local deformation. The bubble so created (prtoein+deformation) executes random walk in the plug. We find that for faster relaxation of the gel, the diffusion of the bubble is greater. Further, on using parameters appropriate for the brush, we find that the diffusion coefficient is much lower. Hence the gel model seems to be more likely explanation for the workings of the plug.

cond-mat.soft

Resonance energy transfer from a fluorescent dye molecule to plasmon and electron-hole excitations of a metal nanoparticle

We study the distance dependence of the rate of electronic excitation energy transfer from a dye molecule to a metal nanoparticle. Using the spherical jellium model, we evaluate the rates corresponding to the excitation of l = 1, 2, and 3 modes of the nanoparticle. Our calculation takes into account both the electron-hole pair and the plasmon excitations of the nanoparticle. The rate follows conventional R^-6 dependence at large distances while small deviations from this behavior are observed at shorter distances. Within the framework of the jellium model, it is not possible to attribute the experimentally observed d^-4 dependence of the rate to energy transfer to plasmons or e-h pair excitations.

physics.chem-ph

Buckled nano rod - a two state system and its dynamics

We consider a suspended elastic rod under longitudinal compression. The compression can be used to adjust potential energy for transverse displacements from harmonic to double well regime. The two minima in potential energy curve describe two possible buckled states at a particular strain. Using transition state theory (TST) we have calculated the rate of conversion from one state to other. If the strain $ε$ is between $ε_c$ and $4 ε_c$, the saddle point is the straight rod. But for $ε_c < 4 ε_c$, the saddle is S-shaped. At $ε_c = 4 ε_c$ the simple TST rate diverges. We suggest methods to correct this divergence, both for classical and quantum calculations. We also find that zero point energy contributions can be quite large (as large as $10^9$) so that single mode calculations can lead to large errors in the rate.

cond-mat.other

Pulling a polymer out of a potential well and the mechanical unzipping of DNA

Motivated by the experiments on DNA under torsion, we consider the problem of pulling a polymer out of a potential well by a force applied to one of its ends. If the force is less than a critical value, then the process is activated and has an activation energy proportinal to the length of the chain. Above this critical value, the process is barrierless and will occur spontaneously. We use the Rouse model for the description of the dynamics of the peeling out and study the average behaviour of the chain, by replacing the random noise by its mean. The resultant mean-field equation is a nonlinear diffusion equation and hence rather difficult to analyze. We use physical arguments to convert this in to a moving boundary value problem, which can then be solved exactly. The result is that the time $t_{po}$ required to pull out a polymer of $N$ segments scales like $N^2$. For models other than the Rouse, we argue that $t_{po}\sim N^{1+ν}$

cond-mat.soft

Escape of a chain molecule over a barrier - the kink mechanism

We consider the generalization of the Kramers escape over a barrier problem to the case of a long chain molecule. The problem involves the motion of a chain molecule of $N$ segments across a region where the free energy per segment is higher, so that it has to cross a barrier. We consider the limit where the length of the molecule is much larger than the width of the barrier. The width is taken to be sufficiently wide that a coninuum description is applicable to even to the portion over the barrier. We use the Rouse model and analyze the mechanism of crossing a barrier. There can be two dominant mechanisms. They are: end crossing and hairpin crossing. We find the free energy of activation for the hairpin crossing is two times that for end crossing. In both cases, the activation energy has a square root dependence on the temperature $T$, leading to a non-Arrhenius form for the rate. We also show that there is a special time dependent solution of the model, which corresponds to a kink in the chain, confined to the region of the barrier. The movement of the polymer from one side to the other is equivalent to the motion of the kink on the chain in the reverse direction. We also consider the translocation of hydrophilic polypeptides across hydrophobic pores, a process that is quite common in biological systems. Biological systems accomplish this by having a hydrophobic signal sequence at the end that goes in first. We find that for such a molecule, the transition state resembles a hook, and this is in agreement with presently accepted view in cell biology.

cond-mat.soft

Adsorption assisted translocation of a chain molecule through a pore in a spherical vesicle

We analyze the free energy for translocation of a polymer from the outside of a spherical vesicle to the inside. The process is assumed to be driven by the adsorption of the polymer on the inner surface of the vesicle. We argue that in the case where the polymer is adsorbed on the outer surface too, the entropic barrier for translocation is absent. We analyze the adsorption energy and find the free energy profile for the process. We argue that the motion corresponds to a polymer crossing a region with a change in free energy per segment. Based upon our earlier analsis of the behaviour of kinks in such a problem, we conclude that the translocation can occur with a crossing time $t_{cross}\sim N$.

cond-mat.soft

Molecular ratchets - verification of the principle of detailed balance

We argue that the recent experiments of Kelly et. al.(Angew. Chem. Int. Ed. Engl. 36, 1866 (1997)) on molecular ratchets, in addition to being in agreement with the second law of thermodynamics, is a test of the principle of detailed balance for the ratchet. We suggest new experiments, using an asymmetric ratchet, to further test the principle. We also point out methods involving a time variation of the temperature to to give it a directional motion.

cond-mat.stat-mech

Kink motion in the Kramers problem for a chain molecule

We consider the generalization of the Kramers escape over a barrier problem to the case of a long chain molecule. It involves the motion of chain molecule of N segments across a region where the free energy per segment is higher, so that it has to cross a barrier. We use the Rouse model and find that the free energy of activation has a square root dependence on the temperature leading to a non-Arrhenius form for the rate. We also show that there is a special time dependent solution of the model, which corresponds to a kink in the chain, confined to the region of the barrier. The polymer goes from one side to the other by the motion of the kink in the reverse direction. If there is no free energy difference between the two sides of the barrier, then the kink moves by diffusion and the time of crossing t_{cross}~ N^2/T^{3/2}. If there is a free energy difference, then the kink moves with a non-zero velocity from the lower free energy side to the otherleading to t_{cross} ~ N/sqrt{T}.

cond-mat.soft