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Biological water is an ionic solution containing both monovalent and divalent ions. However, the effects of divalent ions on the dynamics of biological water remain largely unknown. Here, we investigate how the transport dynamics of water…

The extant versions of many basal ganglia models use a `gating' model of dopamine function which enhances input to D1 receptor units and attenuates input to D2 receptor units. There is evidence that this model is unsatisfactory because (a)…

In this paper, we present the design and the analysis of an electrochemical circuit for measuring the concentrations of therapeutic drugs using structure-switching aptamers. Aptamers are single-stranded nucleic acids, whose sequence is…

This paper presents a dual-aptamer scheme to cancel the signal drifts from structure-switching aptamers during long-term monitoring. Electrochemical aptamer-based (E-AB) biosensors recently demonstrated their great potential for in vivo…

Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…

In biological cells and novel diagnostic devices biochemical receptors need to be sensitive to extremely small concentration changes of signaling molecules. The accuracy of such molecular signaling is ultimately limited by the counting…

Dopamine levels are linked to neurological illnesses like Parkinson's and Alzheimer's. Thus, reliable and sensitive detection of dopamine is crucial for early diagnosis and surveillance of neurodegenerative diseases. Non-noble-metal-based…

This contribution introduces a neural-network-based approach to discover meaningful transition pathways underlying complex biomolecular transformations in coherence with the committor function. The proposed path-committor-consistent…

Aptamers are chemically produced oligonucleotides, able to bind a variety of targets such as drugs, proteins and pathogens with high sensitivity and selectivity. Therefore, aptamers are largely employed for producing label-free biosensors,…

Living cells sense noisy biochemical signals crucial for survival, yet models incorporating intracellular signaling are limited. This study examines how cells sense chemotactic concentrations through phosphorylation readouts in Ca2+…

Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…

The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…

We calculate experimentally measurable signatures of quantum correlations in a coupled molecular dimer that strongly interacts with its vibrational environment. We investigate intensity and mode-resolved photon coincidences for different…

Nucleic acid-based drugs like aptamers have recently demonstrated great therapeutic potential. However, experimental platforms for aptamer screening are costly, and the scarcity of labeled data presents a challenge for supervised methods to…

The physical limit with which a cell senses external ligand concentration corresponds to the perfect absorber, where all ligand particles are absorbed and overcounting of same ligand particles does not occur. Here we analyze how the lateral…

We present a highly efficient molecular dynamics scheme for calculating the concentration depth profile of dopants in ion irradiated materials. The scheme incorporates several methods for reducing the computational overhead, plus a rare…

Glutamate and glycine are important neurotransmitters in the brain. An action potential prop- agating in the terminal of a presynatic neuron causes the release of glutamate and glycine in the synapse by vesicles fusing with the cell…

In molecular simulations, one of the most difficult points is to track the real dynamics of many-body systems from the first principle. The present study shows that step-size dependences have an unexpected effect on simulation results, even…

We explore the distribution in space and time of a single-photon excitation shared by a network of dipole-dipole interacting atoms that are also coupled to a common photonic field mode. Time-averaged distributions reveal partial trapping of…

Detailed understanding of the role of single dopant atoms in host materials has been crucial for the continuing miniaturization in the semiconductor industry as local charging and trapping of electrons can completely change the behaviour of…