Daniel S. Kosov

Peptide conformational heterogeneity revealed from nonlinear vibrational spectroscopy and molecular-dynamics simulations

Nonlinear time-resolved vibrational spectroscopy is used to compare spectral broadening of the amide I band of the small peptide trialanine with that of N-methylacetamide, a commonly used model system for the peptide bond. In contrast to N-methylacetamide, the amide I band of trialanine is significantly inhomogeneously broadened. Employing classical molecular-dynamics simulations combined with density-functional-theory calculations, the origin of the spectral inhomogeneity is investigated. While both systems exhibit similar hydrogen-bonding dynamics, it is found that the conformational dynamics of trialanine causes a significant additional spectral broadening. In particular, transitions between the poly(Gly)II and the αR conformations are identified as the main source of the additional spectral inhomogeneity of trialanine. The experimental and computational results suggest that trialanine adopts essentially two conformations: poly(Gly)II (80%) and αR (20%). The potential of the joint experimental and computational approach to explore conformational dynamics of peptides is discussed.

Out-of-equilibrium catalysis of chemical reactions by electronic tunnel currents

We present an escape rate theory for current-induced chemical reactions. We use Keldysh nonequilibrium Greens functions to derive a Langevin equation for the reaction coordinate. Due to the out of equilibrium electronic degrees of freedom, the friction, noise, and effective temperature in the Langevin equation depend locally on the reaction coordinate. As an example, we consider the dissociation of diatomic molecules induced by the electronic current from a scanning tunnelling microscope tip. In the resonant tunnelling regime, the molecular dissociation involves two processes which are intricately interconnected: a modification of the potential energy barrier and heating of the molecule. The decrease of the molecular barrier (i.e., the current induced catalytic reduction of the barrier) accompanied by the appearance of the effective, reaction-coordinate-dependent temperature is an alternative mechanism for current-induced chemical reactions, which is distinctly different from the usual paradigm of pumping vibrational degrees of freedom.

Adsorption of lactic acid on chiral Pt surfaces--a density functional theory study.

The adsorption of the chiral molecule lactic acid on chiral Pt surfaces is studied by density functional theory calculations. First, we study the adsorption of L-lactic acid on the flat Pt(111) surface. Using the optimed PBE - van der Waals (oPBE-vdW) functional, which includes van der Waals forces on an ab initio level, it is shown that the molecule has two binding sites, a carboxyl and the hydroxyl oxygen atoms. Since real chiral surfaces are (i) known to undergo thermal roughening that alters the distribution of kinks and step edges but not the overall chirality and (ii) kink sites and edge sites are usually the energetically most favored adsorption sites, we focus on two surfaces that allow qualitative sampling of the most probable adsorption sites. We hereby consider chiral surfaces exhibiting (111) facets, in particular, Pt(321) and Pt(643). The binding sites are either both on kink sites-which is the case for Pt(321) or on one kink site-as on Pt(643). The binding energy of the molecule on the chiral surfaces is much higher than on the Pt(111) surface. We show that the carboxyl group interacts more strongly than the hydroxyl group with the kink sites. The results indicate the possible existence of very small chiral selectivities of the order of 20 meV for the Pt(321) and Pt(643) surfaces. L-lactic acid is more stable on Pt(321)(S) than D-lactic acid, while the chiral selectivity is inverted on Pt(643)(S). The most stable adsorption configurations of L- and D-lactic acid are similar for Pt(321) but differ for Pt(643). We explore the impact of the different adsorption geometries on the work function, which is important for field ion microscopy.

Waiting time distribution for electron transport in a molecular junction with electron-vibration interaction

On the elementary level, electronic current consists of individual electron tunnelling events that are separated by random time intervals. The waiting time distribution is a probability to observe the electron transfer in the detector electrode at time t+τ given that an electron was detected in the same electrode at an earlier time t. We study waiting time distribution for quantum transport in a vibrating molecular junction. By treating the electron-vibration interaction exactly and molecule-electrode coupling perturbatively, we obtain the master equation and compute the distribution of waiting times for electron transport. The details of waiting time distributions are used to elucidate microscopic mechanism of electron transport and the role of electron-vibration interactions. We find that as nonequilibrium develops in the molecular junction, the skewness and dispersion of the waiting time distribution experience stepwise drops with the increase of the electric current. These steps are associated with the excitations of vibrational states by tunnelling electrons. In the strong electron-vibration coupling regime, the dispersion decrease dominates over all other changes in the waiting time distribution as the molecular junction departs far away from the equilibrium.

Distribution of tunnelling times for quantum electron transport

In electron transport, the tunnelling time is the time taken for an electron to tunnel out of a system after it has tunnelled in. We define the tunnelling time distribution for quantum processes in a dissipative environment and develop a practical approach for calculating it, where the environment is described by the general Markovian master equation. We illustrate the theory by using the rate equation to compute the tunnelling time distribution for electron transport through a molecular junction. The tunnelling time distribution is exponential, which indicates that Markovian quantum tunnelling is a Poissonian statistical process. The tunnelling time distribution is used not only to study the quantum statistics of tunnelling along the average electric current but also to analyse extreme quantum events where an electron jumps against the applied voltage bias. The average tunnelling time shows distinctly different temperature dependence for p- and n-type molecular junctions and therefore provides a sensitive tool to probe the alignment of molecular orbitals relative to the electrode Fermi energy.

Nonequilibrium configuration interaction method for transport in correlated quantum systems

We present a new approach to treat correlations in nonequilibrium quantum many-particle system. The method is based on ideas of configuration interaction theory of exact nonperturbative ground state electronic structure calculations. We use superoperator techniques in Liouville–Fock space and represent the nonequilibrium density matrix as a linear combination of all possible nonequilibrium quasiparticle excitations built on the appropriate reference state. As an example we consider the electron transport through the system with electron–phonon interaction. The concept of embedding (buffer zones between the reservoirs and the correlated quantum system) is used to derive an exact master equation for the reduced density matrix. Using approximate (truncated) expansion of the trial density matrix we obtain the linear system of equations for two-quasiparticle amplitudes. Then we compute the steady-state current and compare the result with other approaches. The current conserving property of the method is proven.

Non-renewal statistics for electron transport in a molecular junction with electron-vibration interaction

Quantum transport of electrons through a molecule is a series of individual electron tunneling events separated by stochastic waiting time intervals. We study the emergence of temporal correlations between successive waiting times for the electron transport in a vibrating molecular junction. Using the master equation approach, we compute the joint probability distribution for waiting times of two successive tunneling events. We show that the probability distribution is completely reset after each tunneling event if molecular vibrations are thermally equilibrated. If we treat vibrational dynamics exactly without imposing the equilibration constraint, the statistics of electron tunneling events become non-renewal. Non-renewal statistics between two waiting times τ1 and τ2 means that the density matrix of the molecule is not fully renewed after time τ1 and the probability of observing waiting time τ2 for the second electron transfer depends on the previous electron waiting time τ1. The strong electron-vibration coupling is required for the emergence of the non-renewal statistics. We show that in the Franck-Condon blockade regime, extremely rare tunneling events become positively correlated.

Superoperator coupled cluster method for nonequilibrium density matrix

We develop a superoperator coupled cluster method for nonequilibrium open many-body quantum systems described by the Lindblad master equation. The method is universal and applicable to systems of interacting fermions, bosons or their mixtures. We present a general theory and consider its application to the problem of quantum transport through the system with electron-phonon correlations. The results are assessed against the perturbation theory and nonequilibrium configuration interaction theory calculations.

Solvent induced current-voltage hysteresis and negative differential resistance in molecular junctions

We consider a single molecule circuit embedded into solvent. The Born dielectric solvation model is combined with Keldysh nonequilibrium Greens functions to describe the electron-transport properties of the system. Depending on the dielectric constant, the solvent induces multiple nonequilibrium steady states with corresponding hysteresis in molecular current-voltage characteristics as well as negative differential resistance. We identify the physical range of solvent and molecular parameters where the effects are present. The position of the negative differential resistance peak can be controlled by the dielectric constant of the solvent.

Linear response theory for symmetry improved two particle irreducible effective actions

We investigate the linear response of an O(N) scalar quantum field theory subject to external perturbations using the symmetry-improved two-particle irreducible effective action (SI-2PIEA) formalism [A. Pilaftsis and D. Teresi, Nucl. Phys. B874, 594 (2013)]. Despite satisfactory equilibrium behavior, we find a number of unphysical effects at the linear response level. Goldstone boson field fluctuations are overdetermined, with the only consistent solution being to set the fluctuations and their driving sources to zero, except for momentum modes where the Higgs and Goldstone self-energies obey a particular relationship. Also Higgs field fluctuations propagate masslessly, despite the Higgs propagator having the correct mass. These pathologies are independent of any truncation of the effective action and still exist even if we relax the overdetermining Ward identities, so long as the constraint is formulated O(N) covariantly. We discuss possible reasons for the apparent incompatibility of the constraints and linear response approximation and possible ways forward.