Replica Symmetry Breaking in an Axial Model of Quadrupolar Glass

We investigate the replica symmetry breaking (RSB) in a neighborhood of the instability point of the replica-symmetric solution in the axial quadrupolar glass model. We show that the solution with the first-stage RSB is stable against the subsequent RSB. Although there is no reflection symmetry, the first-stage RSB solution continuously bifurcates from the replica-symmetric one. This implies that our model does not belong to either of the two classes into which spin glasses are usually divided.     

Directed polymers in Hartree-Fock approximation

A replica trick is used to map the problem of directed polymers into a quantum mechanics problem ofn-body bound states. This bound-state problem is then treated using a self-consistent method of Hartree-Fock. Ford=2, the exact result of the DP exponents is reproduced; and for complex DP, the ground-state energyE _n n² is found, confirming previous numerical results.     

The spherical-model limit in a random field

The spherical-model limitn of then-vector model in a random field, with either a statistically independent distribution or with long-range correlated random fields, is studied to demonstrate the correctness of the replica method in which then and replica limits limits are interchanged, provided the replica and thermodynamic limits are taken in the right order, in the case of long-range correlated random fields. A scaling form for the two-point correlation function relevant to the first-order phase transition below the lower critical dimensionality of the random system is also obtained.     

The mean spherical model in a random external field and the replica method

We provide a quick elementary solution of the mean spherical model in a random external field. This also allows an immediate proof of the self-averaging property of the free energy. We calculate the free energy by means of the replica method, i.e., for any (not necessarily integer) replica numbern, and show that when a phase transition occurs the limits andn 0 are not interchangeable.     

Application of torsion angle molecular dynamics for efficient sampling of protein conformations

We investigate the application of torsion angle molecular dynamics (TAMD) to augment conformational sampling of peptides and proteins. Interesting conformational changes in proteins mainly involve torsional degrees of freedom. Carrying out molecular dynamics in torsion space does not only explicitly sample the most relevant degrees of freedom, but also allows larger integration time steps with elimination of the bond and angle degrees of freedom. However, the covalent geometry needs to be fixed during internal coordinate dynamics, which can introduce severe distortions to the underlying potential surface in the extensively parameterized modern Cartesian-based protein force fields. A "projection" approach (Katritch et al. J Comput Chem 2003, 24, 254-265) is extended to construct an accurate internal coordinate force field (ICFF) from a source Cartesian force field. Torsion crossterm corrections constructed from local molecular fragments, together with softened van der Waals and electrostatic interactions, are used to recover the potential surface and incorporate implicit bond and angle flexibility. MD simulations of dipeptide models demonstrate that full flexibility in both the backbone phi/psi and side chain chi1 angles are virtually restored. The efficacy of TAMD in enhancing conformational sampling is then further examined by folding simulations of small peptides and refinement experiments of protein NMR structures. The results show that an increase of several fold in conformational sampling efficiency can be reliably achieved. The current study also reveals some complicated intrinsic properties of internal coordinate dynamics, beyond energy conservation, that can limit the maximum size of the integration time step and thus the achievable gain in sampling efficiency.     

Two‐dimensional replica‐exchange method for predicting protein–ligand binding structures

We have developed a two‐dimensional replica‐exchange method for the prediction of protein–ligand binding structures. The first dimension is the umbrella sampling along the reaction coordinate, which is the distance between a protein binding pocket and a ligand. The second dimension is the solute tempering, in which the interaction between a ligand and a protein and water is weakened. The second dimension is introduced to make a ligand follow the umbrella potential more easily and enhance the binding events, which should improve the sampling efficiency. As test cases, we applied our method to two protein‐ligand complex systems (MDM2 and HSP 90‐alpha). Starting from the configuration in which the protein and the ligand are far away from each other in each system, our method predicted the ligand binding structures in excellent agreement with the experimental data from Protein Data Bank much faster with the improved sampling efficiency than the replica‐exchange umbrella sampling method that we have previously developed. © 2013 Wiley Periodicals, Inc.     

Oversampling Free Energy Perturbation Simulation in Determination of the Ligand-Binding Free Energy

Determination of the ligand-binding affinity is an extremely interesting problem. Normally, the free energy perturbation (FEP) method provides an appropriate result. However, it is of great interest to improve the accuracy and precision of this method. In this context, temperature replica exchange molecular dynamics implementation of the FEP computational approach, which we call replica exchange free energy perturbation (REP) was proposed. In particular, during REP simulations, the system can easily escape from being trapped in local minima by exchanging configurations with high temperatures, resulting in significant improvement in the accuracy and precision of protein–ligand binding affinity calculations. The distribution of the decoupling free energy was enlarged, and its mean values were decreased. This results in changes in the magnitude of the calculated binding free energies as well as in alteration in the binding mechanism. Moreover, the REP correlation coefficient with respect to experiment ( R^REP = 0.85 ± 0.15 ) is significantly boosted in comparison with the FEP one ( R^FEP = 0.64 ± 0.30 ). Furthermore, the root-mean-square error (RMSE) of REP is also smaller than FEP, RMSE^REP = 4.28 ± 0.69 versus RMSE^FEP = 5.80 ± 1.11 kcal/mol, respectively. © 2019 Wiley Periodicals, Inc.     

Theoretical approaches to the glass transition in simple liquids

Theoretical approaches to the development of an understanding of the behaviour of simple supercooled liquids near the structural glass transition are reviewed and our work on this problem, based on the density functional theory of freezing and replicated liquid state theory, are summarized in this context. A few directions for further work on this problem are suggested.     

On the Distribution of Overlaps in the Sherrington–Kirkpatrick Spin Glass Model

This paper describes some of the analytic tools developed recently by Ghirlanda and Guerra in the investigation of the distribution of overlaps in the Sherrington–Kirkpatrick spin glass model and of Parisi's ultrametricity. In particular, we introduce to this task a simplified (but also generalized) model on which the Gaussian analysis is made easier. Moments of the Hamiltonian and derivatives of the free energy are expressed as polynomials of the overlaps. Under the essential tool of self-averaging, we describe with full rigour, various overlap identities and replica independence that actually hold in a rather large generality. The results are presented in a language accessible to probabilists and analysts.