相关论文: Single-molecule experiments in biological physics:…
A molecular dynamics simulation is performed to investigate spatial scale of low energy excitation (LEE) in a single linear chain of united atoms. The self part of the dynamic structure function, $S_\mathrm{S}(q,\omega)$, is obtained in a…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
SMeagol is a software tool to simulate highly realistic microscopy data based on spatial systems biology models, in order to facilitate development, validation, and optimization of advanced analysis methods for live cell single molecule…
In this work we study theoretically the coupling of single molecule magnets (SMMs) to a variety of quantum circuits, including microwave resonators with and without constrictions and flux qubits. The main results of this study is that it is…
Single molecule fluorescence tracking provides information at nm-scale and ms-temporal resolution about the dynamics and interaction of individual molecules in a biological environment. While the dynamic behavior of isolated molecules can…
Localization of single fluorescent molecules is key for physicochemical and biophysical measurements such as single-molecule tracking and super-resolution imaging by single-molecule localization microscopy (SMLM). Recently a series of…
Single-molecule detection enables direct observation of individual biomolecular events, providing mechanistic insights into biological processes and offering a powerful tool for disease diagnostics. However, the fundamental scale mismatch…
We developed a multiscale approach (MultiSCAAL) that integrates the potential of mean force (PMF) obtained from all-atomistic molecular dynamics simulations with a knowledge-based energy function for coarse-grained molecular simulations in…
The turn of the millennium has seen a growing interest in the study of live cells by infrared (IR) spectroscopy, driven by the versatility, wealth of molecular information, and potential for high-throughput screening of the technique.…
Scanning probe microscopy (SPM) investigations of on-surface chemistry on passivated silicon have only shown in-plane chemical reactions, and studies on bare silicon are limited in facilitating additional reactions…
Development and homeostasis in multicellular systems both require exquisite control over spatial molecular pattern formation and maintenance. Advances in spatially-resolved and high-throughput molecular imaging methods such as multiplexed…
This chapter provides a brief introduction to the theory and practice of spatial stochastic simulations. It begins with an overview of different methods available for biochemical simulations highlighting their strengths and limitations.…
Low-energy electron microscopy (LEEM) is a surface science method that works primarily in the UHV environment. It provides information complementary to the other established techniques: it extends the limited view of scanning probe…
A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic…
Single-molecule F\"orster resonance energy transfer (smFRET) is increasingly being used to determine distances, structures, and dynamics of biomolecules in vitro and in vivo. However, generalized protocols and FRET standards ensuring both…
High energy physics aims to understand the fundamental laws of particles and their interactions at both the largest and smallest scales of the universe. This typically means probing very high energies or large distances or using…
Biomolecular force fields have been traditionally derived based on a mixture of reference quantum chemistry data and experimental information obtained on small fragments. However, the possibility to run extensive molecular dynamics…
It is often difficult to quantitatively determine if a new molecular simulation algorithm or software properly implements sampling of the desired thermodynamic ensemble. We present some simple statistical analysis procedures to allow…
Recent advances in scanning transmission electron microscopy (STEM) instrumentation have made it possible to focus electron beams with sub-atomic precision and to identify the chemical structure of materials at the level of individual…
Molecules containing short-lived, radioactive nuclei are uniquely positioned to enable a wide range of scientific discoveries in the areas of fundamental symmetries, astrophysics, nuclear structure, and chemistry. Recent advances in the…