Related papers: Blind analysis of molecular dynamics
Tight-binding (TB) molecular dynamics (MD) has emerged as a powerful method for investigating the atomic-scale structure of materials --- in particular the interplay between structural and electronic properties --- bridging the gap between…
In this paper we show that a dynamical description of the protein folding process provides an effective representation of equilibrium properties and it allows for a direct investigation of the mechanisms ruling the approach towards the…
Empirical scoring functions based on either molecular force fields or cheminformatics descriptors are widely used, in conjunction with molecular docking, during the early stages of drug discovery to predict potency and binding affinity of a…
Continuous monitoring is becoming more popular due to its significant benefits, including reducing sample sizes and reaching earlier conclusions. In general, it involves monitoring nuisance parameters (e.g., the variance of outcomes) until…
A subspace projection to improve channel estimation in massive multi-antenna systems is proposed and analyzed. Together with power-controlled hand-off, it can mitigate the pilot contamination problem without the need for coordination among…
We propose a general alternating minimization algorithm for nonconvex optimization problems with separable structure and nonconvex coupling between blocks of variables. To fix our ideas, we apply the methodology to the problem of blind…
Dynamics of neutral atoms in nonuniform magnetic fields, typical of quadrupole magnetic traps, is considered by applying an accurate method for solving nonlinear systems of differential equations. This method is more general than the…
Coarse-grained (lattice-) models have a long tradition in aiding efforts to decipher the physical or biological complexity of proteins. Despite the simplicity of these models, however, numerical simulations are often computationally very…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
Prediction of protein-ligand binding affinity is a major goal in drug discovery. Generally, free energy gap is calculated between two states (e.g., ligand binding and unbinding). The energy gap implicitly includes the effects of changes in…
Random heteropolymers do not display the typical equilibrium properties of globular proteins, but are the starting point to understand the physics of proteins and, in particular, to describe their non-native states. So far, they have been…
Agnostic learning of Boolean halfspaces is a fundamental problem in computational learning theory, but it is known to be computationally hard even for weak learning. Recent work [CKKMK24] proposed smoothed analysis as a way to bypass such…
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…
A goal in the kinetic characterization of a macromolecular system is the description of its slow relaxation processes, involving (i) identification of the structural changes involved in these processes, and (ii) estimation of the rates or…
This paper presents a method for investigating, through an automatic procedure, the (lack of) identifiability of parametrized dynamical models. This method takes into account constraints on parameters and returns parameters whose…
In drug discovery, molecular dynamics (MD) simulation for protein-ligand binding provides a powerful tool for predicting binding affinities, estimating transport properties, and exploring pocket sites. There has been a long history of…
Blind equalization is a classic yet open problem. Statistic-based algorithms, such as constant modulus (CM), were widely investigated. One inherent issue with blind algorithms is the phase ambiguity of equalized signals. In this letter, we…
We employ various quantum-mechanical approaches for studying the impact of electric fields on both nonretarded and retarded noncovalent interactions between atoms or molecules. To this end, we apply perturbative and non-perturbative methods…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
Dynamic aperture is an important concept for the study of non-linear beam dynamics in circular accelerators. It describes the extent of the phase-space region where a particle's motion remains bounded over a given number of turns.…