Related papers: The study of water shell structure of double-helic…
Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important…
In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does…
We propose a cell segmentation method for analyzing images of densely clustered cells. The method combines the strengths of marker-controlled watershed transformation and a convolutional neural network (CNN). We demonstrate the method…
Describing the interactions of water molecules is one of the most common, yet critical, tasks in molecular dynamics simulations. Because of its unique properties, hundreds of attempts have been made to construct an ideal interaction…
The peculiar structuring of liquid water stems from a fine-tuned molecular principle embodying the two different interaction demands of the water molecule: The formation of hydrogen bonds or the compensation for coordination defects. Here…
This paper studies the nucleus decomposition problem, which has been shown to be useful in finding dense substructures in graphs. We present a novel parallel algorithm that is efficient both in theory and in practice. Our algorithm achieves…
Predicting the secondary structure of RNA is a core challenge in computational biology, essential for understanding molecular function and designing novel therapeutics. The field has evolved from foundational but accuracy-limited…
Colloidal particles grafted with single-stranded DNA (ssDNA) chains can self-assemble into a number of different crystalline structures, where hybridization of the ssDNA chains creates links between colloids stabilizing their structure.…
Concurrent data structures are the data sharing side of parallel programming. Data structures give the means to the program to store data, but also provide operations to the program to access and manipulate these data. These operations are…
Nonlinear water waves interacting with quasi-one-dimensional, non-uniformly periodic bed profiles are studied numerically in the deep-water regime with the help of approximate equations for envelopes of the forward and backward waves.…
Lipid vesicles composed of a mixture of two types of lipids are studied by intensive Monte-Carlo numerical simulations. The coupling between the local composition and the membrane shape is induced by two different spontaneous curvatures of…
The structural flexibility of nucleic acids plays a key role in many fundamental life processes, such as gene replication and expression, DNA-protein recognition, and gene regulation. To obtain a thorough understanding of nucleic acid…
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule F\"orster resonance…
Some emerging concepts of nuclear structure are overviewed. (1) Background: the many-body quantum structure of atomic nucleus, a complex system comprising protons and neutrons (called nucleons collectively), has been studied largely based…
Many recent studies of liquid-liquid phase separation in biology focus on phase separation as a dynamic control mechanism for cellular function, but it can also result in complex mesoscopic structures. We primarily investigate a model…
This work emphasizes the assets of implementing the distributed computing for the intensive use in computational science devoted to the search of new medicines that could be applied in public healthy problems.
Membrane phase-separation is a mechanism that biological membranes often use to locally concentrate specific lipid species in order to organize diverse membrane processes. Phase separation has also been explored as a tool for the design of…
The DNA double helix is a polyanionic macromolecule that in water solutions is neutralized by metal ions (counterions). The property of the counterions to stabilize the water network (positive hydration) or to make it friable (negative…
I present a Hamiltonian model and a computational method suitable to evaluate structural and thermodynamic properties of helical molecules embedded in crowded environments which may confine the space available to the base pair fluctuations.…
Molecular biology explains function of molecules by their geometrical and electronical structures that are mainly determined by utilization of quantum effects in chemistry. However, further quantum effects are not thought to play any…