Related papers: Massively parallel single-molecule manipulation us…
Global machine learning force fields (MLFFs), that have the capacity to capture collective many-atom interactions in molecular systems, currently only scale up to a few dozen atoms due a considerable growth of the model complexity with…
Atomically-resolved imaging and force measurements using the atomic force microscope (AFM) are performed most commonly in a frequency-modulation (FM) mode. This has led to spectacular results, including direct observation of the atomic…
An optical microscope enables image-based findings and diagnosis on microscopic targets, which is indispensable in many scientific, industrial and medical settings. Majority of microscope users are accustomed to standard benchtop…
Super-resolutive 3D tracking, such as PSF engineering or evanescent field imaging has long been used to track microparticles and to enhance the throughput of single molecules force spectroscopic measurements. However, current methods…
With the invention of scanning probe techniques, direct imaging of single atoms and molecules became possible. Today, scanning tunnelling microscopy (STM) routinely provides angstrom-scale image resolution. At the same time, however, STM…
Nearly all standard force fields employ the 'sum-of-spheres' approximation, which models intermolecular interactions purely in terms of interatomic distances. Nonetheless, atoms in molecules can have significantly non-spherical shapes,…
We propose a new multi-scale molecular dynamics simulation method which can achieve high accuracy and high sampling efficiency simultaneously without aforehand knowledge of the coarse grained (CG) potential and test it for a biomolecular…
The study of biomolecular folding has been greatly advanced by single-molecule force spectroscopy (SMFS), which enables the observation of the dynamics of individual molecules. However, extracting quantitative models of fundamental…
Centrifugation is a commonly performed laboratory procedure that helps to separate blood cells such as $RBCs$, $WBCs$, and platelets from plasma or serum. Although centrifugation is a routine procedure in most medical laboratories, the…
A force field is a critical component in molecular dynamics simulations for computational drug discovery. It must achieve high accuracy within the constraints of molecular mechanics' (MM) limited functional forms, which offers high…
We develop a novel parallel resampling algorithm for fully parallelized particle filters, which is designed with GPUs (graphics processing units) or similar parallel computing devices in mind. With our new algorithm, a full cycle of…
Atomic force microscopy (AFM) has been constantly supporting nanosciences and nanotechnologies for over 30 years, being present in many fields from condensed matter physics to biology. It enables measuring very weak forces at the nanoscale,…
Numerous cell types relate to their immediate environment by exerting a three-dimensional pressure field on their environment, with components both longitudinal and transverse to the cell membrane. This pressure field can in principle be…
Traction Force Microscopy (TFM) computes the forces exerted at the surface of an elastic material by measuring induced deformations in volume. It is used to determine the pattern of the adhesion forces exerted by cells or by cellular…
Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In…
Single-cell proteomics (SCP) is transforming our understanding of biological complexity by shifting from bulk proteomics, where signals are averaged over thousands of cells, to the proteome analysis of individual cells. This granular…
Most technical polymers and many biopolymers contain very different molecular species (unlike chain length, molecular architecture and/or chemical composition) in contrast to pure low molecular weight compounds. This inconsistent…
Time-lapse fluorescent microscopy (TLFM) combined with predictive mathematical modelling is a powerful tool to study the inherently dynamic processes of life on the single-cell level. Such experiments are costly, complex and labour…
Human physiology and pathology arise from the coordinated interactions of diverse single cells. However, analyzing single cells has been limited by the low sensitivity and throughput of analytical methods. DNA sequencing has recently made…
Atomic force microscopy (AFM) is a powerful tool to investigate interaction forces at the micro and nanoscale. Cantilever stiffness, dimensions and geometry of the tip can be chosen according to the requirements of the specific application,…