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G. Garberoglio

Publications and source records attributed to G. Garberoglio.

9 recordsLinked to original sources
arXiv2011

Quantum Diffusive Dynamics of Macromolecular Transitions

We study the role of quantum fluctuations of atomic nuclei in the real-time dynamics of non-equilibrium macro-molecular transitions. To this goal we introduce an extension of the Dominant Reaction Pathways (DRP) formalism, in which the quantum corrections to the classical overdamped Langevin dynamics are rigorously taken into account to order h^2 . We first illustrate our approach in simple cases, and compare with the results of the instanton theory. Then we apply our method to study the C7_eq to C7_ax transition of alanine dipeptide. We find that the inclusion of quantum fluctuations can significantly modify the reaction mechanism for peptides. For example, the energy difference which is overcome along the most probable pathway is reduced by as much as 50%.

physics.bio-ph↗
arXiv2010

Dominant folding pathways of a peptide chain, from ab-initio quantum-mechanical simulations

Using the Dominant Reaction Pathways method, we perform an ab-initio quantum-mechanical simulation of a conformational transition of a peptide chain. The method we propose makes it possible to investigate the out-of-equilibrium dynamics of these systems, without resorting to an empirical representation of the molecular force field. It also allows to study rare transitions involving rearrangements in the electronic structure. By comparing the results of the ab-initio simulation with those obtained employing a standard force field, we discuss its capability to describe the non-equilibrium dynamics of conformational transitions.

q-bio.BM↗
arXiv2010

A path integral for heavy-quarks in a hot plasma

We propose a model for the propagation of a heavy-quark in a hot plasma, to be viewed as a first step towards a full description of the dynamics of heavy quark systems in a quark-gluon plasma, including bound state formation. The heavy quark is treated as a non relativistic particle interacting with a fluctuating field, whose correlator is determined by a hard thermal loop approximation. This approximation, which concerns only the medium in which the heavy quark propagates, is the only one that is made, and it can be improved. The dynamics of the heavy quark is given exactly by a quantum mechanical path integral that is calculated in this paper in the Euclidean space-time using numerical Monte Carlo techniques. The spectral function of the heavy quark in the medium is then reconstructed using a Maximum Entropy Method. The path integral is also evaluated exactly in the case where the mass of the heavy quark is infinite; one then recovers known results concerning the complex optical potential that controls the long time behavior of the heavy quark. The heavy quark correlator and its spectral function is also calculated semi-analytically at the one-loop order, which allows for a detailed description of the coupling between the heavy quark and the plasma collective modes.

hep-ph↗
arXiv2009

Ab-initio Dynamics of Rare Thermally Activated Reactions

We introduce a framework to investigate ab-initio the dynamics of rare thermally activated reactions. The electronic degrees of freedom are described at the quantum-mechanical level in the Born-Oppenheimer approximation, while the nuclear degrees of freedom are coupled to a thermal bath, through a Langevin equation. This method is based on the path integral representation for the stochastic dynamics and yields the time evolution of both nuclear and electronic degrees of freedom, along the most probable reaction pathways, without spending computational time to explore metastable states. This approach is very efficient and allows to study thermally activated reactions which cannot be simulated using ab-initio molecular dynamics techniques. As a first illustrative application, we characterize the dominant pathway in the cyclobutene to butadiene reaction.

cond-mat.mes-hall↗
arXiv2008

Boltzmann bias grand canonical Monte Carlo

We derive an efficient method for the insertion of structured particles in grand canonical Monte Carlo simulations of adsorption in very confining geometries. We extend this method to path integral simulations and use it to calculate the isotherm of adsorption of hydrogen isotopes in narrow carbon nanotubes (2D confinement) and slit pores (1D confinement) at the temperatures of 20 K and 77 K, discussing its efficiency by comparison to the standard path integral grand canonical Monte Carlo algorithm. We use this algorithm to perform multicomponent simulations in order to calculate the hydrogen isotope selectivity for adsorption in narrow carbon nanotubes and slit pores at finite pressures. The algorithm described here can be applied to the study of adsorption of real oligomers and polymers in narrow pores and channels.

cond-mat.stat-mech↗
arXiv2007

Hybrid path integral Monte Carlo simulation of rigid diatomic molecules: effect of quantized rotations on the selectivity of hydrogen isotopes in carbon nanotubes

We present a multiple time step algorithm for hybrid path integral Monte Carlo simulations involving rigid linear rotors. We show how to calculate the quantum torques needed in the simulation from the rotational density matrix, for which we develop an approximate expression suitable in the case of heteronuclear molecules. We use this method to study the effect of rotational quantization on the quantum sieving properties of carbon nanotubes, with particular emphasis to the para-T2/para-H2 selectivity at 20 K. We show how to treat classically only some of the degrees of freedom of the hydrogen molecule and we find that in the limit of zero pressure the quantized nature of the rotational degrees of freedom greatly influence the selectivity, especially in the case of the (3,6) nanotube, which is the narrowest tube that we have studied. We also use path integral Monte Carlo simulations to calculate adsorption isotherms of different hydrogen isotopes in the interior of carbon nanotubes and the corresponding selectivity at finite pressures. It is found that the selectivity increases with respect to the zero pressure value and tends to a constant value at saturation. We use a simplified effective harmonic oscillator model to discuss the origin of this behavior.

cond-mat.stat-mech↗
arXiv2007

Quantitative Protein Dynamics from Dominant Folding Pathways

We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding problem are removed and simulating the entire reaction in atomistic details using existing computers becomes feasible. In addition, this formalism provides a natural framework to investigate the relationships between thermodynamical and kinetic aspects of the folding. For example, it is possible to show that, in order to have a large probability to remain unchanged under Langevin diffusion, the native state has to be characterized by a small conformational entropy. We discuss how to determine the most probable folding pathway, to identify configurations representative of the transition state and to compute the most probable transition time. We perform an illustrative application of these ideas, studying the conformational evolution of alanine di-peptide, within an all-atom model based on the empiric GROMOS96 force field.

q-bio.QM↗
arXiv2000

Instantaneous Normal Mode analysis of liquid HF

We present an Instantaneous Normal Modes analysis of liquid HF aimed to clarify the origin of peculiar dynamical properties which are supposed to stem from the arrangement of molecules in linear hydrogen-bonded network. The present study shows that this approach is an unique tool for the understanding of the spectral features revealed in the analysis of both single molecule and collective quantities. For the system under investigation we demonstrate the relevance of hydrogen-bonding ``stretching'' and fast librational motion in the interpretation of these features.

cond-mat.soft↗