Related papers: Exploring Conformational Landscapes Along Anharmon…
All biological systems are subject to perturbations: due to thermal fluctuations, external environments, or mutations. Yet, while biological systems are composed of thousands of interacting components, recent high-throughput experiments…
Computational modelling offers a cost-effective and time-efficient alternative to experimental studies in biomedical engineering. In cardiac electro-mechanics, finite element method (FEM)-based simulations provide valuable insights into…
Accurately simulating molecular vibronic spectra remains computationally challenging due to the exponential scaling of required calculations. Here, we show that employing the linear coupling model within the gaussian boson sampling…
We describe a new approach based on semiclassical molecular dynamics that allows to simulate infrared absorption or emission spectra of molecular systems with inclusion of anharmonic intensities. This is achieved from semiclassical power…
Harnessing the power of low-dimensional materials in thermal applications calls for a solid understanding of the anomalous thermal properties of such systems. We analyze thermal conduction in one-dimensional systems by determining the…
FEMSIM, a Fortran code, has been developed to simulate the fluctuation electron microscopy signal, the variance, V(k), from a model atomic structure. FEMSIM has been incorporated into a hybrid-reverse Monte Carlo code that combines an…
We present calculations on the damping of a low-frequency adsorbate mode on a metal surface, namely the frustrated translation of Na on Cu(100). For the first time, vibrational lifetimes of excited adlayers are extracted from…
Force distance curves (FCs) are among the most direct measurements performed in atomic force microscopy (AFM), yet their information content is often reduced by filtering and quasi-static interpretation. Here, enabled by a new…
We expand iterative numerically-exact influence functional path-integral tools and present a method capable of following the nonequilibrium time evolution of subsystems coupled to multiple bosonic and fermionic reservoirs simultaneously.…
Understanding how the effectiveness of natural photosynthetic energy harvesting systems arises from the interplay between quantum coherence and environmental noise represents a significant challenge for quantum theory. Recently it has begun…
Developing efficient path integral (PI) methods for atomistic simulations of vibrational spectra in heterogeneous condensed phases and interfaces has long been a challenging task. Here, we present the h-CMD method, short for hybrid centroid…
We present a simple and efficient method to incorporate anharmonic effects in the vibrational \textcolor{black}{analyses} of molecules within density functional theory (DFT) calculations. This approach is closely related to the traditional…
In this paper, we introduce a new adaptive data analysis method to study trend and instantaneous frequency of nonlinear and non-stationary data. This method is inspired by the Empirical Mode Decomposition method (EMD) and the recently…
In addition to thermal noise, which is essential to promote conformational transitions in biopolymers, cellular environment is replete with a spectrum of athermal fluctuations that are produced from a plethora of active processes. To…
In this paper, adaptive non-uniform compressive sampling (ANCS) of time-varying signals, which are sparse in a proper basis, is introduced. ANCS employs the measurements of previous time steps to distribute the sensing energy among…
Detecting conformational transitions in molecular systems is key to understanding biological processes. Here, we investigate the force variance in single-molecule pulling experiments as an indicator of molecular folding transitions. We…
Fractional models and their parameters are sensitive to changes in the intrinsic micro-structures of anomalous materials. We investigate how such physics-informed models propagate the evolving anomalous rheology to the nonlinear dynamics of…
As a step towards a more realistic modeling of vibrations in single-molecule devices, we investigate the effects of charge-dependent vibrational frequencies and anharmonic potentials on electronic transport. For weak phonon relaxation, we…
Exquisite sensitivities are a prominent advantage of quantum sensors. Ramsey sequences allow precise measurement of direct current fields, while Hahn-echo-like sequences measure alternating current fields. However, the latter are restrained…
Flow matching models have emerged as a powerful framework for realistic image generation by learning to reverse a corruption process that progressively adds Gaussian noise. However, because noise is injected in the latent domain, its impact…