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Latent spaces offer an efficient and effective means of summarizing data while implicitly preserving meta-information through relational encoding. We leverage these meta-embeddings to develop a modality-agnostic, unified encoder. Our method…
The analysis of spatial data from biological imaging technology, such as imaging mass spectrometry (IMS) or imaging mass cytometry (IMC), is challenging because of a competitive sampling process which convolves signals from molecules in a…
The out-of-plane fluctuations of carbon atoms in a graphene sheet have been studied by means of classical molecular dynamic simulations with an empirical force-field as a function of temperature. The Fourier analysis of the out-of-plane…
Automated chemical synthesis, materials fabrication, and spectroscopic physical measurements often bring forth the challenge of process trajectory optimization, i.e., discovering the time dependence of temperature, electric field, or…
Molecular transitions -- such as protein folding, allostery, and membrane transport -- are central to biology yet remain notoriously difficult to simulate. Their intrinsic rarity pushes them beyond reach of standard molecular dynamics,…
The performance of Hamiltonian Monte Carlo simulations crucially depends on both the integration timestep and the number of integration steps. We present an adaptive general-purpose framework to automatically tune such parameters, based on…
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…
Spontaneous structural rearrangements play a central role in the organization and function of complex biomolecular systems. In principle, physics-based computer simulations like Molecular Dynamics (MD) enable us to investigate these…
Quantum simulation in its current state faces experimental overhead in terms of physical space and cooling. We propose boson sampling as an alternative compact synthetic platform performing at room temperature. Identifying the capability of…
The life of a cell is governed by highly dynamical microscopic processes. Two notable examples are the diffusion of membrane receptors and the kinetics of transcription factors governing the rates of gene expression. Different fluorescence…
This work is devoted to quantifying how periodic perturbation can change the rate of metastable transition in stochastic mechanical systems with weak noises. A closed-form explicit expression for approximating the rate change is provided,…
Low-order thermoacoustic models are qualitatively correct, but they are typically quantitatively inaccurate. We propose a time-domain bias-aware method to make qualitatively low--order models quantitatively (more) accurate. First, we…
We investigate correlations between low-frequency vibrational modes and rearrangements in two-dimensional colloidal glasses composed of thermosensitive microgel particles which readily permit variation of sample packing fraction. At each…
Terahertz time-domain spectroscopy and differential scanning calorimetry were used to study the role of the dynamics of biomolecules decoupled from solvent effects. Lyophilised sucrose exhibited steadily increasing absorption with…
Anisotropic barostats are employed to carry out Molecular Dynamics simulations where the volume is allowed to fluctuate with no constraints on the shape of the simulation cell. Most of these algorithms are based on second-order differential…
Theoretical frameworks used to qualitatively and quantitatively describe nuclear dynamics in solids are often based on the harmonic approximation. However, this approximation is known to become inaccurate or to break down completely in many…
On the basis of the self-consistent phonon theory and the special displacement method, we develop an approach for the treatment of anharmonicity in solids. We show that this approach enables the efficient calculation of…
A novel method for the numerical prediction of the slowly varying dynamics of nonlinear mechanical systems has been developed. The method is restricted to the regime of an isolated nonlinear mode and consists of a two-step procedure: In the…
Transport and mixing properties of aperiodic flows are crucial to a dynamical analysis of the flow, and often have to be carried out with limited information. Finite-time coherent sets are regions of the flow that minimally mix with the…
Fluorescence spectroscopy is an image correlation technique to analyze and characterize the molecular dynamics from a sequence of fluorescence images. Many image correlation techniques have been developed for different applications [1]. But…