arXiv subjects

Vladimir Privman

Publications and source records attributed to Vladimir Privman.

At least 55 records · Page 3Linked to original sources

arXiv2010

Biochemical Filter with Sigmoidal Response: Increasing the Complexity of Biomolecular Logic

The first realization of a designed, rather than natural, biochemical filter process is reported and analyzed as a promising network component for increasing the complexity of biomolecular logic systems. Key challenge in biochemical logic research has been achieving scalability for complex network designs. Various logic gates have been realized, but a "toolbox" of analog elements for interconnectivity and signal processing has remained elusive. Filters are important as network elements that allow control of noise in signal transmission and conversion. We report a versatile biochemical filtering mechanism designed to have sigmoidal response in combination with signal-conversion process. Horseradish peroxidase-catalyzed oxidation of chromogenic electron donor by hydrogen peroxide, was altered by adding ascorbate, allowing to selectively suppress the output signal, modifying the response from convex to sigmoidal. A kinetic model was developed for evaluation of the quality of filtering. The results offer improved capabilities for design of scalable biomolecular information processing systems.

physics.bio-ph↗

arXiv2010

Realization and Properties of Biochemical-Computing Biocatalytic XOR Gate Based on Signal Change

We consider a realization of the XOR logic gate in a system involving two competing biocatalytic reactions, for which the logic-1 output is defined by these two processes causing a change in the optically detected signal. A model is developed for describing such systems in an approach suitable for evaluation of the analog noise amplification properties of the gate and optimization of its functioning. The initial data are fitted for gate quality evaluation within the developed model, and then modifications are proposed and experimentally realized for improving the gate functioning.

cond-mat.soft↗

arXiv2010

Morphology of Nanoclusters and Nanopillars Formed in Nonequilibrium Surface Growth for Catalysis Applications

We consider growth of nanoclusters and nanopillars in a model of surface deposition and restructuring yielding morphologies of interest in designing catalysis applications. Kinetic Monte Carlo numerical modeling yields examples of the emergence of FCC-symmetry surface features, allowing evaluation of the fraction of the resulting active sites with desirable properties, such as (111)-like coordination, as well as suggesting the optimal growth regimes.

cond-mat.soft↗

arXiv2010

Enzymatic AND Logic Gates Operated Under Conditions Characteristic of Biomedical Applications

Experimental and theoretical analyses of the lactate dehydrogenase and glutathione reductase based enzymatic AND logic gates in which the enzymes and their substrates serve as logic inputs are performed. These two systems are examples of the novel, previously unexplored, class of biochemical logic gates that illustrate potential biomedical applications of biochemical logic. They are characterized by input concentrations at logic 0 and 1 states corresponding to normal and abnormal physiological conditions. Our analysis shows that the logic gates under investigation have similar noise characteristics. Both significantly amplify random noise present in inputs, however we establish that for realistic widths of the input noise distributions, it is still possible to differentiate between the logic 0 and 1 states of the output. This indicates that reliable detection of abnormal biomedical conditions is indeed possible with such enzyme-logic systems.

cond-mat.soft↗

arXiv2010

Models of Synthesis of Uniform Colloids and Nanocrystals

We present modeling approaches to explain mechanisms of control of uniformity (narrow distribution) of sizes and shapes in synthesis of nanosize crystals and micron-size colloids. We consider those situations when the nanocrystals are formed by burst nucleation. The colloids are then self-assembled by aggregation of nanocrystals. The coupled kinetic processes are both controlled by diffusional transport, yielding well-defined colloid dispersions used in many applications. We address aspects of modeling of particle structure selection, ranging from nucleation to growth by aggregation and to mechanisms of emergence of particle shapes.

cond-mat.soft↗

arXiv2010

Error-Control and Digitalization Concepts for Chemical and Biomolecular Information Processing Systems

We consider approaches for controlling the buildup of noise by design of gates for chemical and biomolecular computing, in order to realize stable, scalable networks for multi-step information processing. Solvable rate-equation models are introduced and used to illustrate several recently developed concepts and methodologies. We also outline future challenges and possible research directions.

physics.bio-ph↗

arXiv2009

Enzyme-Based Logic Systems for Information Processing

We review enzymatic systems which involve biocatalytic reactions utilized for information processing (biocomputing). Extensive ongoing research in biocomputing, mimicking Boolean logic gates has been motivated by potential applications in biotechnology and medicine. Furthermore, novel sensor concepts have been contemplated with multiple inputs processed biochemically before the final output is coupled to transducing "smart-material" electrodes and other systems. These applications have warranted recent emphasis on networking of biocomputing gates. First few-gate networks have been experimentally realized, including coupling, for instance, to signal-responsive electrodes for signal readout. In order to achieve scalable, stable network design and functioning, considerations of noise propagation and control have been initiated as a new research direction. Optimization of single enzyme-based gates for avoiding analog noise amplification has been explored, as were certain network-optimization concepts. We review and exemplify these developments, as well as offer an outlook for possible future research foci. The latter include design and uses of non-Boolean network elements, e.g., filters, as well as other developments motivated by potential novel sensor and biotechnology applications.

physics.bio-ph↗

arXiv2009

Towards Biosensing Strategies Based on Biochemical Logic Systems

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 resulting systems to smart/responsive electrodes for output readout, have opened new biosensing opportunities. Here we survey existing enabling research results, as well as ideas and research avenues for future development of a new paradigm of digitally operating biosensors logically processing multiple biochemical signals through Boolean logic networks composed of biomolecular reactions, yielding the final output signals as YES/NO responses. Such systems can lead to high-fidelity biosensing compared to common single or parallel sensing devices.

physics.bio-ph↗

arXiv2009

Topics in Quantum Dynamics and Coherence for Quantum Information Processing

We outline selected trends and results in theoretical modeling of quantum systems in support of the developing research field of quantum information processing. The resulting modeling tools have been applied to semiconductor materials and nanostructures that show promise for implementation of coherent, controlled quantum dynamics at the level of registers of several quantum bits (qubits), such as spins. Many-body field-theoretical techniques have been utilized to address a spectrum of diverse research topics. Specifically, the theory of decoherence and more generally the origin and effects of quantum noise and the loss of entanglement in quantum dynamics of qubits and several-qubit registers has been advanced. Qubit coupling mechanisms via the indirect exchange interaction have been investigated, and quantum computing designs have been evaluated for scalability. We outline general and specific research challenges, the solution of which will advance the field of modeling "open quantum systems" to further our understanding of how environmental influences affect quantum coherence and its loss during quantum dynamics.

cond-mat.mes-hall↗

arXiv2009

Enzymatic AND-Gate Based on Electrode-Immobilized Glucose-6-Phosphate Dehydrogenase: Towards Digital Biosensors and Biochemical Logic Systems with Low Noise

Electrode-immobilized glucose-6-phosphate dehydrogenase is used to catalyze an enzymatic reaction which carries out the AND logic gate. This logic function is considered here in the context of biocatalytic processes utilized for the biocomputing applications for "digital" (threshold) sensing/actuation. We outline the response functions desirable for such applications and report the first experimental realization of a sigmoid-shape response in one of the inputs. A kinetic model is developed and utilized to evaluate the extent to which the experimentally realized gate is close to optimal.

q-bio.MN↗

arXiv2009

Shape Selection in Diffusive Growth of Colloids and Nanoparticles

We report numerical investigations of a three-dimensional model of diffusive growth of fine particles, the internal structure of which corresponds to different crystal lattices. A growing cluster (particle) is immersed in, and exchanges monomer building blocks with a surrounding medium of diffusing (off-lattice) monomers. On-surface dynamics of the latter is accounted for by allowing, in addition to detachment, monomer motion to the neighboring vacant crystal sites, according to probabilistic rules mimicking local thermalization. The key new feature of our model is the focus on the growth of a single cluster, emerging as a crystalline core, without development of defects that can control large-scale growth modes. This single, defect-free core growth is imposed by the specific dynamical rules assumed. Our results offer a possible explanation of the experimentally observed shape uniformity, i.e., fixed, approximately even-sized proportions, in synthesis of uniform colloids and nanoparticles. We demonstrate the basic principles of well-defined particle shape emergence in such growth. Specifically, several shapes are possible for a given crystal structure. Formation of shapes that follow the crystal symmetry and are uniform, can be a result of the nonequilibrium nature of the growth process. The shape of a growing particle can be controlled by varying the relative rates of kinetic processes, as well as by adjusting the concentration of monomers in the surrounding medium.

cond-mat.stat-mech↗

arXiv2009

Analog Noise Reduction in Enzymatic Logic Gates

In this work we demonstrate both experimentally and theoretically that the analog noise generation by a single enzymatic logic gate can be dramatically reduced to yield gate operation with virtually no input noise amplification. This is achieved by exploiting the enzyme's specificity when using a co-substrate that has a much lower affinity than the primary substrate. Under these conditions, we obtain a negligible increase in the noise output from the logic gate as compared to the input noise level. Experimental realizations of the AND logic gate with the enzyme horseradish peroxidase using hydrogen peroxide and two different co-substrates, 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid) (ABTS) and ferrocyanide, with vastly different rate constants confirmed our general theoretical conclusions.

q-bio.MN↗

arXiv2009

Optimization of Enzymatic Logic Gates and Networks for Noise Reduction and Stability

Biochemical computing attempts to process information with biomolecules and biological objects. In this work we review our results on analysis and optimization of single biochemical logic gates based on enzymatic reactions, and a network of three gates, for reduction of the "analog" noise buildup. For a single gate, optimization is achieved by analyzing the enzymatic reactions within a framework of kinetic equations. We demonstrate that using co-substrates with much smaller affinities than the primary substrate, a negligible increase in the noise output from the logic gate is obtained as compared to the input noise. A network of enzymatic gates is analyzed by varying selective inputs and fitting standardized few-parameters response functions assumed for each gate. This allows probing of the individual gate quality but primarily yields information on the relative contribution of the gates to noise amplification. The derived information is then used to modify experimental single gate and network systems to operate them in a regime of reduced analog noise amplification.

q-bio.MN↗

arXiv2009

Shape Selection in Synthesis of Colloids and Nanoparticles

We address a long-standing problem in colloid and nanoparticle science: particle shape selection in solution synthesis. Our main finding is that a proper balance of two processes, preferential attachment of transported monomers at the protruding features of the growing cluster and monomer rearrangement at the cluster surface, can yield a well-defined particle shape for a large interval of times, and persisting for sizes much larger than the original seed.

cond-mat.soft↗

arXiv2009

Random Sequential Adsorption of Oriented Superdisks

In this work we extend recent study of the properties of the dense packing of "superdisks," by Y. Jiao, F. H. Stillinger and S. Torquato, Phys. Rev. Lett. 100, 245504 (2008), to the jammed state formed by these objects in random sequential adsorption. The superdisks are two-dimensional shapes bound by the curves of the form |x|^(2p) + |y|^(2p) = 1, with p > 0. We use Monte Carlo simulations and theoretical arguments to establish that p = 1/2 is a special point at which the jamming density has a discontinuous derivative as a function of p. The existence of this point can be also argued for by geometrical arguments.

cond-mat.stat-mech↗

arXiv2008

Network Analysis of Biochemical Logic for Noise Reduction and Stability: A System of Three Coupled Enzymatic AND Gates

We develop an approach aimed at optimizing the parameters of a network of biochemical logic gates for reduction of the "analog" noise buildup. Experiments for three coupled enzymatic AND gates are reported, illustrating our procedure. Specifically, starch - one of the controlled network inputs - is converted to maltose by beta-amylase. With the use of phosphate (another controlled input), maltose phosphorylase then produces glucose. Finally, nicotinamide adenine dinucleotide (NAD+) - the third controlled input - is reduced under the action of glucose dehydrogenase to yield the optically detected signal. Network functioning is analyzed by varying selective inputs and fitting standardized few-parameters "response-surface" functions assumed for each gate. This allows a certain probe of the individual gate quality, but primarily yields information on the relative contribution of the gates to noise amplification. The derived information is then used to modify our experimental system to put it in a regime of a less noisy operation.

q-bio.MN↗

arXiv2008

Synthesis of Silver Colloids: Experiment and Computational Model

We summarize our recent results that model the formation of uniform spherical silver colloids prepared by mixing iso-ascorbic acid and silver-amine complex solutions in the absence of dispersants. We found that the experimental results can be modeled effectively by the two-stage formation mechanism used previously to model the preparation of colloidal gold spheres. The equilibrium concentration of silver atoms and the surface tension of silver precursor nanocrystals are both treated as free parameters, and the experimental reaction time scale is fit by a narrow region of this two-parameter space. The kinetic parameter required to match the final particle size is found to be very close to that used previously in modeling the formation of uniform gold particles, suggesting that similar kinetics governs the aggregation process. The model also reproduces semi quantitatively the effects of temperature and solvent viscosity on particle synthesis.

cond-mat.soft↗

arXiv2008

Random Sequential Adsorption of Objects of Decreasing Size

We consider the model of random sequential adsorption, with depositing objects, as well as those already at the surface, decreasing in size according to a specified time dependence, from a larger initial value to a finite value in the large time limit. Numerical Monte Carlo simulations of two-dimensional deposition of disks and one-dimensional deposition of segments are reported for the density-density correlation function and gap-size distribution function, respectively. Analytical considerations supplement numerical results in the one-dimensional case. We investigate the correlation hole - the depletion of correlation functions near contact and, for the present model, their vanishing at contact - that opens up at finite times, as well as its closing and reemergence of the logarithmic divergence of correlation properties at contact in the large time limit.

math-ph↗