Related papers: Analysis tools for single-monomer measurements of …
Accurate knowledge of absorption coefficient of a sample is a prerequisite for measuring the third order optical nonlinearity of materials, which can be a serious limitation for unknown samples. We introduce a method, which measures both…
In this work we used dissipative particle dynamics simulations to study the copolymerization process in the presence of spatial heterogeneities caused by incompatibility between polymerizing monomers. The polymer sequence details as well as…
A general problem of current interest is the analysis of diffusion problems in singularly perturbed domains, within which small subdomains are removed from the domain interior and boundary conditions imposed on the resulting holes. One…
Knowledge of a protein's atomic conformational ensemble is critical to determining its function, yet state-of-the-art ensemble prediction models are limited by lack of high-quality conformational data from simulation or experiment. Recent…
In order to study linker-mediated aggregation of colloidal particles with limited valence, we combine kinetic Monte Carlo simulations and an approximate theory based on the Smoluchowski equations. We found that aggregation depends strongly…
Single-molecule pulling techniques have emerged as versatile tools for probing the noncovalent forces holding together the secondary and tertiary structure of macromolecules. They also constitute a way to study at the single-molecule level…
Many processes of scientific importance are characterized by time scales that extend far beyond the reach of standard simulation techniques. To circumvent this impediment a plethora of enhanced sampling methods has been developed. One…
Single-pixel imaging has emerged as a key technique in fluorescence microscopy, where fast acquisition and reconstruction are crucial. In this context, images are reconstructed from linearly compressed measurements. In practice, total…
We adapted existing polymer growth strategies for equilibrium sampling of peptides described by modern atomistic forcefields with implicit solvent. The main novel feature of our approach is the use of pre-calculated statistical libraries of…
An approach that combines Self-Organizing maps, hierarchical clustering and network components is presented, aimed at comparing protein conformational ensembles obtained from multiple Molecular Dynamic simulations. As a first result the…
Cells rely on focal adhesions (FAs) to carry out a variety of important tasks, including motion, environmental sensing, and adhesion to the extracellular matrix. Although attaining a fundamental characterization of FAs is a compelling goal,…
Building structures with hierarchical order through the self-assembly of smaller blocks is not only a prerogative of nature, but also a strategy to design artificial materials with tailored functions. We explore in simulation the…
Monte Carlo (MC) Simulations, Differential Scanning Calorimetry (DSC) and Fourier Transform InfraRed (FTIR) spectroscopy were used to study the melting behavior of single lipid components in two-component membranes of…
We present the checkpoint ensembles method that can learn ensemble models on a single training process. Although checkpoint ensembles can be applied to any parametric iterative learning technique, here we focus on neural networks. Neural…
We propose a hybrid Molecular Dynamics/Multi-particle Collision Dynamics model to simulate a set of self-assembled semiflexible filaments and free monomers. Further, we introduce a Monte-Carlo scheme to deal with single monomer addition…
Over recent years, super-resolution and single-molecule imaging methods have delivered unprecedented details on the nanoscale organization and dynamics of individual molecules in different contexts. Yet, visualizing single-molecule…
Single-molecule fluorescence spectroscopy is a powerful method that avoids ensemble averaging, but its temporal resolution is limited by the fluorescence lifetime to nanoseconds at most. At the ensemble level, two-dimensional spectroscopy…
Advances in experimental techniques and in theoretical models have improved our understanding of protein crystallization. But they have also left open questions regarding the protein phase behavior and self-assembly kinetics, such as why…
Image processing and pattern recognition offer a useful and versatile method for optically characterizing drops of a colloidal solution during the drying process and in its final state. This paper exploits image processing techniques…
The process of gathering and associating data from multiple sensors or sub-detectors due to a common physical event (the process of event-building) is used in many fields, including high-energy physics and $\gamma$-ray astronomy. Fault…