Related papers: Blind analysis of molecular dynamics

A major impediment to a more complete understanding of barrier crossing and other single-molecule processes is the inability to directly visualize the trajectories and dynamics of atoms and molecules in reactions. Rather, the kinetics are…

Molecular docking that predicts the bound structures of small molecules (ligands) to their protein targets, plays a vital role in drug discovery. However, existing docking methods often face limitations: they either overlook crucial…

Entanglement is a fundamental property of quantum systems, essential for non-trivial quantum programs. Identifying when qubits become entangled is critical for circuit optimization, and for arguing for the correctness of quantum algorithms.…

In this paper, we introduce a new algorithm based on archetypal analysis for blind hyperspectral unmixing, assuming linear mixing of endmembers. Archetypal analysis is a natural formulation for this task. This method does not require the…

Blind deconvolution is the problem of recovering a sharp image and a blur kernel from a noisy blurry image. Recently, there has been a significant effort on understanding the basic mechanisms to solve blind deconvolution. While this effort…

Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from the insensitivity to the geometrical…

Blind system identification is known to be an ill-posed problem and without further assumptions, no unique solution is at hand. In this contribution, we are concerned with the task of identifying an ARX model from only output measurements.…

Predicting a ligand's bound pose to a target protein is a key component of early-stage computational drug discovery. Recent developments in machine learning methods have focused on improving pose quality at the cost of model runtime. For…

A major challenge in nonadiabatic molecular dynamics is to automatically and objectively identify the key reaction coordinates that drive molecules toward distinct excited-state decay channels. Traditional manual analyses are inefficient…

We present a simple model of protein folding dynamics that captures key qualitative elements recently seen in all-atom simulations. The goals of this theory are to serve as a simple formalism for gaining deeper insight into the physical…

The output of molecular dynamics simulations is high-dimensional, and the degrees of freedom among the atoms are related in intricate ways. Therefore, a variety of analysis frameworks have been introduced in order to distill complex motions…

Blind ptychography is the scanning version of coherent diffractive imaging which seeks to recover both the object and the probe simultaneously. Based on alternating minimization by Douglas-Rachford splitting, AMDRS is a blind ptychographic…

We propose a computational method to quantitatively evaluate the systematic uncertainties that arise from undetectable sources in biological measurements using live-cell imaging techniques. We then demonstrate this method in measuring…

Learning how proteins fold will hardly have any impact in the way conventional -- active site centered -- drugs are designed. On the other hand, this knowledge is proving instrumental in defining a new paradigm for the identification of…

Understanding protein dynamics are essential for deciphering protein functional mechanisms and developing molecular therapies. However, the complex high-dimensional dynamics and interatomic interactions of biological processes pose…

Accelerated molecular dynamics (MD) simulations are implemented to model the sliding process of AFM experiments at speeds close to those found in experiment. In this study the hyperdynamics method, originally devised to extend MD time…

Simulations are vital for understanding and predicting the evolution of complex molecular systems. However, despite advances in algorithms and special purpose hardware, accessing the timescales necessary to capture the structural evolution…

Mixed-quantum-classical molecular dynamics simulation implies an effective measurement on the electronic states owing to continuously tracking the atomic forces.Based on this insight, we propose a quantum trajectory mean-field approach for…

Psychological bias towards, or away from, a prior measurement or a theory prediction is an intrinsic threat to any data analysis. While various methods can be used to avoid the bias, e.g. actively not looking at the result, only data…

Linear dynamical systems are a fundamental and powerful parametric model class. However, identifying the parameters of a linear dynamical system is a venerable task, permitting provably efficient solutions only in special cases. This work…