Related papers: A Numerical Study of Three-Armed DNA Hydrogel Stru…
The field of complex self-assembly is moving toward the design of multi-particle structures consisting of thousands of distinct building blocks. To exploit the potential benefits of structures with such `addressable complexity,' we need to…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…
In many organisms, homologous (or repetitive) chromosomal regions can associate or/and undergo concerted epigenetic changes in the absence of DNA breakage and recombination. The direct specific pairing of DNA duplexes with similar…
The traditional nuclear shell model approach is extended to include many-body forces. The empirical Hamiltonian with a three-body force is constructed for the identical nucleons on the 0f7/2 shell. Manifestations of the three-body force in…
We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)] originally designed to reproduce the properties of DNA molecules with…
Generative models have achieved impressive results in many domains including image and text generation. In the natural sciences, generative models have led to rapid progress in automated drug discovery. Many of the current methods focus on…
Motivated by recent experiments we have studied the optical conductivity of DNA in its natural environment containing water molecules and counter ions. Our density functional theory calculations (using SIESTA) for four base pair B-DNA with…
This paper describes the model for DNA in MATLAB taking into account all of component atoms. In this model, it is possible to generate sequences with length 10000 basis pairs available for introducing all types of sequences. Once the…
Colloidal gels consist of percolating networks of interconnected arms. Their mechanical properties depend on the individual arms, and on their collective behaviour. We use numerical simulations to pull on a single arm, built from a model…
At the cutting edge of materials science, matter is designed to self-organize into structures that perform a wide range of functions. The past two decades have witnessed major innovations in the versatility of building blocks, ranging from…
All-atom simulations have become increasingly popular to study conformational and dynamical properties of nucleic acids as they are accurate and provide high spatial and time resolutions. This high resolution however comes at a heavy…
A model for the motion of ring-shaped DNA in a gel is introduced and studied by numerical simulations and a mean-field approximation. The ring motion is mediated by finger-shaped loops (hernias) that move in an amoeba-like fashion around…
We present a novel technique of sampling the configurations of helical proteins. Assuming knowledge of native secondary structure, we employ assembly rules gathered from a database of existing structures to enumerate the geometrically…
DNA flexibility is a key determinant of biological function, from nucleosome positioning to transcriptional regulation, motivating a direct measurement of the bend-torque response of individual DNA molecules. In this work, DNA bending is…
In this Letter, we present a simple model of aqueous interfacial molecular structure and we use this model to isolate the effects of hydrogen bonding on the dielectric properties of the liquid water-vapor interface. By comparing this model…
We employ a large scale molecular simulation based on bond-order ReaxFF to simulate the chemical reaction and study the damage to a large fragment of DNA-molecule in the solution by ionizing radiation. We illustrate that the randomly…
The computational modelling of DNA is becoming crucial in light of new advances in DNA nanotechnology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single…
The combination of self-assembly and electronic properties as well as its true nanoscale dimensions make DNA a promising candidate for a building block of single molecule electronics. We argue that the intrinsic double helix conformation of…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
We present direct evidence for a reversible phase transition of DNA-linked colloidal gold assemblies. Transmission electron microscopy and optical absorption spectroscopy are used to monitor the colloidal gold phase transition, whose…