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Free energy landscapes decisively determine the progress of enzymatically catalyzed reactions[1]. Time-resolved macromolecular crystallography unifies transient-state kinetics with structure determination [2-4] because both can be…
DNA sequences are prone to creating secondary structures by folding back on themselves by non-specific hybridization among its nucleotides. The formation of secondary structures makes the sequences chemically inactive towards synthesis and…
We present an exact enumeration algorithm for identifying the {\it native} configuration - a maximally compact self avoiding walk configuration that is also the minimum energy configuration for a given set of contact-energy schemes; the…
We propose an application of molecular information theory to analyze the folding of single domain proteins. We analyze results from various areas of protein science, such as sequence-based potentials, reduced amino acid alphabets, backbone…
We propose coding techniques that limit the length of homopolymers runs, ensure the GC-content constraint, and are capable of correcting a single edit error in strands of nucleotides in DNA-based data storage systems. In particular, for…
Parts of DNA sequences known as exons and introns play very different role in coding and storage of genetic information. Here we show that their conducting properties are also very different. Taking into account long-range correlations…
Chemical reactions inside cells occur in compartment volumes in the range of atto- to femtolitres. Physiological concentrations realized in such small volumes imply low copy numbers of interacting molecules with the consequence of…
DNA is an attractive candidate for data storage. Its millennial durability and nanometer scale offer exceptional data density and longevity. Its relevance to medical applications also drives advances in DNA-related biotechnology. To protect…
We generate non-lattice packings of spheres in up to 22 dimensions using the geometrical constraint satisfaction algorithm RRR. Our aggregated data suggest that it is easy to double the density of Ball's lower bound, and more tentatively,…
Security proofs in quantum cryptography rely on conditional entropies. In a many-round protocol, their estimation is a challenging task; one must account for the most general attacks by an eavesdropper, including those that are not…
The process of DNA-based data storage (DNA storage for short) can be mathematically modelled as a communication channel, termed DNA storage channel, whose inputs and outputs are sets of unordered sequences. To design error correcting codes…
We develop revised theoretical ideas on the mechanism by which the transcription factor proteins locate their specific binding sites on DNA faster than the three-dimensional (3D) diffusion controlled rate limit. We demonstrate that the…
Knowledge present in a domain is well expressed as relationships between corresponding concepts. For example, in zoology, animal species form complex hierarchies; in genomics, the different (parts of) molecules are organized in groups and…
Using Brownian dynamics simulations, we study the migration of long charged chains in an electrophoretic microchannel device consisting of an array of microscopic entropic traps with alternating deep regions and narrow constrictions. Such a…
The concept of the reduced set of contact maps is introduced. Using this concept we find the ground state candidates for Hydrophobic-Polar lattice model on a two dimensional square lattice. Using these results we exactly enumerate the…
The thermodynamic properties of DNA circular molecules are investigated by a new path integral computational method which treats in the real space the fundamental forces stabilizing the molecule. The base pair and stacking contributions to…
The Binomial channel serves as a fundamental model for molecular communication (MC) systems employing molecule-counting receivers. Here, deterministic identification (DI) is addressed for the discrete-time Binomial channels (DTBC), subject…
The hydrophobic/polar HP model on the square lattice has been widely used to investigate basics of protein folding. In the cases where all designing sequences (sequences with unique ground states) were enumerated without restrictions on the…
Beyond the genetic code, there is another layer of information encoded as chemical modifications on histone proteins positioned along the DNA. Maintaining these modifications is crucial for survival and identity of cells. How the…
In this work we start the investigation of tight complexity bounds for connectivity problems parameterized by cutwidth assuming the Strong Exponential-Time Hypothesis (SETH). Van Geffen et al. posed this question for odd cycle transversal…