Francesco Pederiva

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 are removed, and simulating the entire reaction in atomistic details using existing computers becomes feasible. We discuss how to determine the most probable folding pathway, identify configurations representative of the transition state, and compute the most probable transition time. We perform an illustrative application of these ideas, studying the conformational evolution of alanine dipeptide, within an all-atom model based on the empiric GROMOS96 force field.

Diffusion Monte Carlo study of circular quantum dots

Dipartimento di Fisica and INFM, Universit`a di Trento, I-38050 Povo,Trento, Italy(February 1, 2008)We present ground and excited state energies obtained from Diffusion Monte Carlo (DMC)calculations, using accurate multiconfiguration wave functions, for N electrons (N ≤ 13) confinedto a circular quantum dot. We compare the density and correlation energies to the predictionsof local spin density approximation theory (LSDA), and Hartree-Fock theory (HF), and analyzethe electron-electron pair-correlation functions. The DMC estimated change in electrochemicalpotential as a function of the number of electrons in the dot is compared to that from LSDA andHF calculations. Hund’s first rule is found to be satisfied for all dots except N = 4 for which thereis a near degeneracy.85.30.Vw,73.61.-rI. INTRODUCTION

Puckering free energy of pyranoses: A NMR and metadynamics-umbrella sampling investigation.

We present the results of a combined metadynamics-umbrella sampling investigation of the puckered conformers of pyranoses described using the GROMOS 45a4 force field. The free energy landscape of Cremer-Pople puckering coordinates has been calculated for the whole series of α and β aldohexoses, showing that the current force field parameters fail in reproducing proper puckering free energy differences between chair conformers. We suggest a modification to the GROMOS 45a4 parameter set which improves considerably the agreement of simulation results with theoretical and experimental estimates of puckering free energies. We also report on the experimental measurement of altrose conformer populations by means of NMR spectroscopy, which show good agreement with the predictions of current theoretical models.

Quantum Monte Carlo calculation of the equation of state of neutron matter

We calculated the equation of state of neutron matter at zero temperature by means of the auxiliary field diffusion Monte Carlo (AFDMC) method combined with a fixed-phase approximation. The calculation of the energy was carried out by simulating up to 114 neutrons in a periodic box. Special attention was given to reducing finite-size effects at the energy evaluation by adding to the interaction the effect due to the truncation of the simulation box, and by performing several simulations using different numbers of neutrons. The finite-size effects due to kinetic energy were also checked by employing the twist-averaged boundary conditions. We considered a realistic nuclear Hamiltonian containing modern two- and three-body interactions of the Argonne and Urbana family. The equation of state can be used to compare and calibrate other many-body calculations and to predict properties of neutron stars.

Dominant reaction pathways in high-dimensional systems.

This paper is devoted to the development of a theoretical and computational framework denominated dominant reaction pathways (DRPs) to efficiently sample the statistically significant thermally activated reaction pathways, in multidimensional systems. The DRP approach is consistently derived from the Langevin equation through a systematic expansion in the thermal energy, k(B)T. Its main advantage with respect to existing simulation techniques is that it provides a natural and rigorous framework to perform the path sampling using constant displacement steps, rather than constant time steps. In our previous work, we have shown how to obtain the set of most probable reaction pathways, i.e., the lowest order in the k(B)T expansion. In this work, we show how to compute the corrections to the leading order due to stochastic fluctuations around the most probable trajectories. We also discuss how to obtain predictions for the evolution of arbitrary observables and how to generate conformations, which are representative of the transition state ensemble. We illustrate how our method works in practice by studying the diffusion of a point particle in a two-dimensional funneled external potential.This paper is devoted to the development of a theoretical and computational framework to efficiently sample the statistically significant thermally activated reaction pathways, in multidimensional systems obeying Langevin dynamics. We show how to obtain the set of most probable reaction pathways and compute the corrections due to quadratic thermal fluctuations around such trajectories. We discuss how to obtain predictions for the evolution of arbitrary observables and how to generate conformations which are representative of the transition state ensemble. We present an illustrative implementation of our method by studying the diffusion of a point particle in a 2-dimensional funneled external potential.

Equation of State of Superfluid Neutron Matter and the Calculation of the 1S0 Pairing Gap

We present a quantum Monte Carlo study of the zero-temperature equation of state of neutron matter and the computation of the 1S0 pairing gap in the low-density regime with rho < 0.04 fm(-3). The system is described by a nonrelativistic nuclear Hamiltonian including both two- and three-nucleon interactions of the Argonne and Urbana type. This model interaction provides very accurate results in the calculation of the binding energy of light nuclei. A suppression of the gap with respect to the pure BCS theory is found, but sensibly weaker than in other works that attempt to include polarization effects in an approximate way.

Accurate determination of the interaction between Λ hyperons and nucleons from auxiliary field diffusion Monte Carlo calculations

Background: An accurate assessment of the hyperon-nucleon interaction is of great interest in view of recent observations of very massive neutron stars. The challenge is to build a realistic interaction that can be used over a wide range of masses and in infinite matter starting from the available experimental data on the binding energy of light hypernuclei. To this end, accurate calculations of the hyperon binding energy in a hypernucleus are necessary.

Effects of the two-body and three-body hyperon-nucleon interactions in Λ hypernuclei

Background: The calculation of the hyperon binding energy in hypernuclei is crucial to understanding the interaction between hyperons and nucleons.

Microscopic calculation of the equation of state of nuclear matter and neutron star structure

We present results for neutron star models constructed with a new equation of state for nuclear matter at zero temperature. The ground state is computed using the Auxiliary Field Diffusion Monte Carlo (AFDMC) technique, with nucleons interacting via a semiphenomenological Hamiltonian including a realistic two-body interaction. The effect of many-body forces is included by means of additional density-dependent terms in the Hamiltonian. In this letter we compare the properties of the resulting neutron-star models with those obtained using other nuclear Hamiltonians, focusing on the relations between mass and radius, and between the gravitational mass and the baryon number.

On the calculation of puckering free energy surfaces.

Cremer-Pople puckering coordinates appear to be the natural candidate variables to explore the conformational space of cyclic compounds and in literature different parametrizations have been used to this end. However, while every parametrization is equivalent in identifying conformations, it is not obvious that they can also act as proper collective variables for the exploration of the puckered conformations free energy surface. It is shown that only the polar parametrization is fit to produce an unbiased estimate of the free energy landscape. As an example, the case of a six-membered ring, glucuronic acid, is presented, showing the artifacts that are generated when a wrong parametrization is used.