Related papers: Blind analysis of molecular dynamics
In this paper, we study a nonconvex continuous relaxation of MAP inference in discrete Markov random fields (MRFs). We show that for arbitrary MRFs, this relaxation is tight, and a discrete stationary point of it can be easily reached by a…
We study the non-reversibility of molecular dynamics trajectories arising from the amplification of rounding errors. We analyse the causes of such behaviour and give arguments, indicating that this does not pose a significant problem for…
In single-molecule experiments, the dynamics of molecular motors are often observed indirectly by measuring the trajectory of an attached bead in a motor-bead assay. In this work, we propose a method to extract the step size and stalling…
This study employed an artificial intelligence-enhanced molecular simulation framework to enable efficient Path Integral Molecular Dynamics (PIMD) simulations. Owing to its modular architecture and high-throughput capabilities, the…
We introduce NimbleD, an efficient self-supervised monocular depth estimation learning framework that incorporates supervision from pseudo-labels generated by a large vision model. This framework does not require camera intrinsics, enabling…
Amplitude-modulation atomic force microscopy enables observation of fragile molecules at the nanometer scale. To shorten measurement times and capture dynamic molecules, increasing the frame rate is essential. Traditionally, maximum frame…
Accurately measuring cell stiffness is challenging due to the invasiveness of traditional methods like atomic force microscopy (AFM) and optical stretching. We introduce a non-invasive off-axis system using holographic imaging and acoustic…
A new Markov Chain Monte Carlo method for simulating the dynamics of molecular systems characterized by hard-core interactions is introduced. In contrast to traditional Kinetic Monte Carlo approaches, where the state of the system is…
Compressed sensing (CS) is a concept that allows to acquire compressible signals with a small number of measurements. As such it is very attractive for hardware implementations. Therefore, correct calibration of the hardware is a central…
We demonstrate that the recently proposed pruned-enriched Rosenbluth method PERM (P.~Grassberger, Phys.~Rev.~{\bf E 56} (1997) 3682) leads to very efficient algorithms for the folding of simple model proteins. We test it on several models…
How to recognise whether an observed person walks or runs? We consider a dynamic environment where observations (e.g. the posture of a person) are caused by different dynamic processes (walking or running) which are active one at a time and…
We study the motion of discrete interfaces driven by ferromagnetic interactions in a two-dimensional low-contrast periodic environment, by coupling the minimizing movements approach by Almgren, Taylor and Wang and a discrete-to-continuum…
The controlled generation of entangled states and their subsequent detection are integral aspects of quantum information science. In this work, we analyse the application of nonlinear witnesses to the verification of entanglement, and we…
Fourier acceleration has been successfully applied to the simulation of lattice field theories for more than a decade. In this paper, we extend the method to the dynamics of discrete particles moving in continuum. Although our method is…
In this work, we analytically examine the validity of molecular dynamics for a soft potential system by considering a simple one-dimensional system with a piecewise continuous linear repulsive potential wall having a constant slope $a$. We…
In this work, we define a practical identifiability criterion, (e, q)-identifiability, based on a parameter e, reflecting the noise in observed variables, and a parameter q, reflecting the mean-square error of the parameter estimator. This…
We develop sensitivity analyses for weak nulls in matched observational studies while allowing unit-level treatment effects to vary. The methods may be applied to studies using any optimal without-replacement matching algorithm. In contrast…
This paper presents a mathematical framework for characterizing state blocking in discrete event systems (DES) under transition deletions. We introduce a path-based analysis approach that determines whether systems maintain non-blocking…
We describe a method that focuses sampling effort on a user-defined selection of a large system, which can lead to substantial decreases in computational effort by speeding up the calculation of nonbonded interactions. A naive approach can…
Many classical Computer Vision problems, such as essential matrix computation and pose estimation from 3D to 2D correspondences, can be tackled by solving a linear least-square problem, which can be done by finding the eigenvector…