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In chemotaxis, cells are modulating their migration patterns in response to concentration gradients of a guiding substance. Immune cells are believed to use such chemotactic sensing for remotely detecting and homing in on pathogens.…
The full understanding of cellular functions requires information about protein numbers for various biomolecular assemblies and their dynamics, which can be partly accessed by super-resolution fluorescence microscopy. Yet, many protein…
Most sensory cells use cross-membrane chemoreceptors to detect chemical signals in the environment. The biochemical properties and spatial organization of chemoreceptors play important roles in achieving and maintaining sensitivity and…
Simulation of biomolecular networks is now indispensable for studying biological systems, from small reaction networks to large ensembles of cells. Here we present a novel approach for stochastic simulation of networks embedded in the…
Thermodynamic selection is an indirect competition between agents feeding on the same energy resource and obeying the laws of thermodynamics. We examine scenarios of this selection, where the agent is modeled as a heat-engine coupled to two…
Biochemical reaction networks in living cells usually involve reversible covalent modification of signaling molecules, such as protein phosphorylation. Under conditions of small molecule numbers, as is frequently the case in living cells,…
Reaction rate equations are ordinary differential equations that are frequently used to describe deterministic chemical kinetics at the macroscopic scale. At the microscopic scale, the chemical kinetics is stochastic and can be captured by…
It is well-known that biological and social interaction networks have a varying degree of redundancy, though a consensus of the precise cause of this is so far lacking. In this paper, we introduce a topological redundancy measure for…
Understanding the thermodynamic properties of quantum systems is essential for developing energy-efficient quantum technologies. In this regard, this work explores the application of quantum computational methods to study the quantum…
We present a comprehensive characterization of cold molecular beams from a cryogenic buffer-gas cell, providing an insight into the physics of buffer-gas cooling. Cold molecular beams are extracted from a cryogenic cell by electrostatic…
The adaptive immune system provides a diverse set of molecules that can mount specific responses against a multitude of pathogens. Memory is a key feature of adaptive immunity, which allows organisms to respond more readily upon…
There are many problems in biochemistry that are difficult to study experimentally. Simulation methods are appealing due to direct availability of atomic coordinates as a function of time. However, direct molecular simulations are…
Self-replication is a capacity common to every species of living thing, and simple physical intuition dictates that such a process must invariably be fueled by the production of entropy. Here, we undertake to make this intuition rigorous…
Biological regulatory networks depend upon chemical interactions to process information. Engineering such molecular computing systems is a major challenge for synthetic biology and related fields. The chemical reaction network (CRN) model…
Recent advances in biochemical computing, i.e., information processing with cascades of primarily enzymatic reactions realizing computing gates, such as AND, OR, etc., as well as progress in networking these gates and coupling of the…
Recent advances in electronics are enabling substantial processing to be performed at each node (robots, sensors) of a networked system. Local processing enables data compression and may mitigate measurement noise, but it is still slower…
Active constituents burn fuel to sustain individual motion, giving rise to collective effects that are not seen in systems at thermal equilibrium, such as phase separation with purely repulsive interactions. There is a great potential in…
Traditional stochastic modeling of reactive systems limits the domain of applicability of the associated path thermodynamics to systems involving a single elementary reaction at the origin of each observed change in composition. An…
The energy dependent thermoelectric response of a single molecule contains valuable information about its transmission function and its excited states. However, measuring it requires devices that can efficiently heat up one side of the…
In this paper, a diffusion-based molecular communication channel between two nano-machines is considered. The effect of the amount of memory on performance is characterized, and a simple memory-limited decoder is proposed and its…