Searcharxiv⌕ Search

arXiv subjects

Alexei V. Tkachenko

Publications and source records attributed to Alexei V. Tkachenko.

At least 37 records · Page 2Linked to original sources

Conditional emergence of classical domain and branching of quantum histories

We outline the Minimalistic Measurement Scheme (MMS) compatible with regular unitary evolution of a closed quantum system. Within this approach, a part of the system becomes informationally isolated (restricted) which leads to a natural emergence of the classical domain. This measurement scenario is a simpler alternative to environment-induced decoherence. In its basic version, MMS involves two ancilla qubits, $A$ and $X$, entangled with each other and with the System $S$. Informational or thermodynamic cost of measurement is represented by $X$-qubit being isolated, i.e. becoming unavailable for future interactions with the rest of the system. Conditional upon this isolation, $A$-qubit, that plays the role of an Apparatus, becomes classical and records the outcome of the measurement. The procedure may be used to perform von Neumann-style projective measurements or generalized ones, that corresponds to Positive-Operator Value Measure (POVM). By repeating the same generalized measurement multiple times with different $A$- and $X$-qubits, one asymptotically approaches the wave function collapse in the basis determined by the premeasurement process. We present a simple result for the total information extracted after $N$ such weak measurements. Building upon MMS, we propose a construction that maps a history of a quantum system onto a set of $A$-qubits. It resembles the Consistent History (CH) formulation of Quantum Mechanics (QM), but is distinct from it, and is built entirely within the conventional QM. In particular, consistency postulate of CH formalism is not automatically satisfied, but rather is an emerging property. Namely, each measurement event corresponds to the branching of mutually exclusive classical realities whose probabilities are additive. In a general case, however, the superposition between different histories is determined by the history density matrix.

quant-ph↗

Compact interaction potential for van der Waals nanorods

We studied the van der Waals interactions of two finite, solid, cylindrical rods at arbitrary angle and position with respect to each other. An analytic interpolative formula for the interaction potential energy is constructed, based on various asymptotic cases. The potential can be readily used for numerical and analytic description of multi-wall carbon nanotubes, metallic nanorods, rod-shaped colloids, or any other similar objects with significant van der Waals interactions.

cond-mat.soft↗

Onset of natural selection in auto-catalytic heteropolymers

Reduction of information entropy along with ever-increasing complexity are among the key signatures of living matter. Understanding the onset of such behavior in early prebiotic world is essential for solving the problem of origins of life. To elucidate this transition, we study a theoretical model of information-storing heteropolymers capable of template-assisted ligation and subjected to cyclic non-equilibrium driving forces. We discover that this simple physical system undergoes a spontaneous reduction of the information entropy due to the competition of chains for constituent monomers. This natural-selection-like process ultimately results in the survival of a limited subset of polymer sequences. Importantly, the number of surviving sequences remains exponentially large, thus opening up the possibility of further increase in complexity due to Darwinian evolution. We also propose potential experimental implementations of our model using either biopolymers or artificial nano-structures.

q-bio.PE↗

Layer-by-layer assembly of patchy particles as a route to non-trivial structures

We propose a new strategy for robust high-quality self-assembly of non-trivial periodic structures out of patchy particles, and investigate it with Brownian Dynamics (BD) simulations. Its first element is the use of specific patch-patch and shell-shell interactions between the particles, that can be implemented through differential functionalization of patched and shell regions with specific DNA strands. The other key element of our approach is the use of layer-by-layer protocol that allows to avoid a formations of undesired random aggregates. As an example, we design and self-assemble in silico a version of a Double Diamond (DD) lattice in which four particle types are arranged into BCC crystal made of four FCC sub-lattices. The lattice can be further converted to Cubic Diamond (CD) by selective removal of the particles of certain types. Our results demonstrate that by combining the directionality, selectivity of interactions and the layer-by-layer protocol, a high-quality robust self-assembly can be achieved.

cond-mat.soft↗

Onset of autocatalysis of information-coding polymers

Self-replicating systems based on information-coding polymers are of crucial importance in biology. They also recently emerged as a paradigm in material design on nano- and micro-scales. We present a general theoretical and numerical analysis of the problem of spontaneous emergence of autocatalysis for heteropolymers capable of template-assisted ligation driven by cyclic changes in the environment. Our central result is the existence of the first order transition between the regime dominated by free monomers and that with a self-sustaining population of sufficiently long chains. We provide a simple, mathematically tractable model supported by numerical simulations, which predicts the distribution of chain lengths and the onset of autocatalysis in terms of the overall monomer concentration and two fundamental rate constants. Another key result of our study is the emergence of the kinetically-limited optimal overlap length between a template and each of its two substrates. The template-assisted ligation allows for heritable transmission of the information encoded in chain sequences thus opening up the possibility of long-term memory and evolvability in such systems.

cond-mat.soft↗

Chromatic patchy particles: effects of specific interactions on liquid structure

We study the structural and thermodynamic properties of patchy particle liquids, with a special focus on the role of "color", i.e. specific interactions between individual patches. A possible experimental realization of such "chromatic" interactions is by decorating the particle patches with single-stranded DNA linkers. The complementarity of the linkers can promote selective bond formation between predetermined pairs of patches. By using MD simulations, we compare the local connectivity, the bond orientation order, and other structural properties of the aggregates formed by the "colored" and "colorless" systems. The analysis is done for spherical particles with two different patch arrangements (tetrahedral and cubic). It is found that the aggregated (liquid) phase of the "colorless" patchy particles is better connected, denser and typically has stronger local order than the corresponding "colored" one. This, in turn, makes the colored liquid less stable thermodynamically. Specifically, we predict that in a typical case the chromatic interactions should increase the relative stability of the crystalline phase with respect to the disordered liquid, thus expanding its region in the phase diagram.

cond-mat.soft↗

DNA-Programmed Mesoscopic Architecture

We study the problem of the self-assembly of nanoparticles (NPs) into finite mesoscopic structures with a programmed local morphology and complex overall shape. Our proposed building blocks are NPs directionally-functionalized with DNA. The combination of directionality and selectivity of interactions allows one to avoid unwanted metastable configurations which have been shown to lead to slow self-assembly kinetics even in much simpler systems. With numerical simulations, we show that a variety of target mesoscopic objects can be designed and self-assembled in near perfect yield. They include cubes, pyramids, boxes and even an Empire State Building model. We summarize our findings with a set of design strategies that lead to the successful self-assembly of a wide range of mesostructures.

cond-mat.soft↗

Precursors of order in aggregates of patchy particles

We study computationally the local structure of aggregated systems of patchy particles. By calculating the probability distribution functions of various rotational invariants we can identify the precursors of orientation order in amorphous phase. Surprisingly, the strongest signature of local order is observed for 4-patch particles with tetrahedral symmetry, not for 6-patch particles with the cubic one. This trend is exactly opposite to their known ability to crystallize. We relate this anomaly to the observation that a generic aggregate of patchy systems has coordination number close to 4. Our results also suggest a significant correlation between rotational order in the studied liquids with the corresponding crystalline phases, making this approach potentially useful for a broader range of patchy systems.

cond-mat.soft↗

A simple analytical formula for the free-energy of ligand-receptor mediated interactions

Recently \1, we presented a general theory for calculat- ing the strength and properties of colloidal interactions mediated by ligand-receptor bonds (such as those that bind DNA-coated colloids). In this communication, we derive a surprisingly simple analytical form for the inter- action free energy, which was previously obtainable only via a costly numerical thermodynamic integration. As a result, the computational effort to obtain potentials of in- teraction is significantly reduced. Moreover, we can gain insight from this analytic expression for the free energy in limiting cases. In particular, the connection of our general theory to other previous specialised approaches is now made transparent. This important simplification will significantly broaden the scope of our theory.

cond-mat.soft↗

A Generalized Theory of DNA Looping and Cyclization

We have developed a generalized semi-analytic approach for efficiently computing cyclization and looping $J$ factors of DNA under arbitrary binding constraints. Many biological systems involving DNA-protein interactions impose precise boundary conditions on DNA, which necessitates a treatment beyond the Shimada-Yamakawa model for ring cyclization. Our model allows for DNA to be treated as a heteropolymer with sequence-dependent intrinsic curvature and stiffness. In this framework, we independently compute enthlapic and entropic contributions to the $J$ factor and show that even at small length scales $(\sim \ell_{p})$ entropic effects are significant. We propose a simple analytic formula to describe our numerical results for a homogenous DNA in planar loops, which can be used to predict experimental cyclization and loop formation rates as a function of loop size and binding geometry. We also introduce an effective torsional persistence length that describes the coupling between twist and bending of DNA when looped.

q-bio.BM↗

Self-assembling DNA-caged particles: nanoblocks for hierarchical self-assembly

DNA is an ideal candidate to organize matter on the nanoscale, primarily due to the specificity and complexity of DNA based interactions. Recent advances in this direction include the self-assembly of colloidal crystals using DNA grafted particles. In this article we theoretically study the self-assembly of DNA-caged particles. These nanoblocks combine DNA grafted particles with more complicated purely DNA based constructs. Geometrically the nanoblock is a sphere (DNA grafted particle) inscribed inside a polyhedron (DNA cage). The faces of the DNA cage are open, and the edges are made from double stranded DNA. The cage vertices are modified DNA junctions. We calculate the equilibriuim yield of self-assembled, tetrahedrally caged particles, and discuss their stability with respect to alternative structures. The experimental feasability of the method is discussed. To conclude we indicate the usefulness of DNA-caged particles as nanoblocks in a hierarchical self-assembly strategy.

cond-mat.soft↗

How to build nanoblocks using DNA scaffolds

In recent years there have been a number of proposals to utilize the specificity of DNA based interactions for potential applications in nanoscience. One interesting direction is the self-assembly of micro- and nanoparticle clusters using DNA scaffolds. In this letter we consider a DNA scaffold method to self-assemble clusters of "colored" particles. Stable clusters of microspheres have recently been produced by an entirely different method. Our DNA based approach self-assembles clusters with additional degrees of freedom associated with particle permutation. We demonstrate that in the non-equilibrium regime of irreversible binding the self-assembly process is experimentally feasible. These color degrees of freedom may allow for more diverse intercluster interactions essential for hierarchical self-assembly of larger structures.

cond-mat.soft↗

Kinetic limitations of cooperativity based drug delivery systems

We study theoretically a novel drug delivery system that utilizes the overexpression of certain proteins in cancerous cells for cell specific chemotherapy. The system consists of dendrimers conjugated with "keys" (ex: folic acid) which "key-lock" bind to particular cell membrane proteins (ex: folate receptor). The increased concentration of "locks" on the surface leads to a longer residence time for the dendrimer and greater incorporation into the cell. Cooperative binding of the nanocomplexes leads to an enhancement of cell specificity. However, both our theory and detailed analysis of in-vitro experiments indicate that the degree of cooperativity is kinetically limited. We demonstrate that cooperativity and hence the specificity to particular cell type can be increased by making the strength of individual bonds weaker, and suggest a particular implementation of this idea. The implications of the work for optimizing the design of drug delivery vehicles are discussed.

cond-mat.soft↗

Colloids with key-lock interactions: non-exponential relaxation, aging and anomalous diffusion

The dynamics of particles interacting by key-lock binding of attached biomolecules are studied theoretically. Experimental realizations of such systems include colloids grafted with complementary single-stranded DNA (ssDNA), and particles grafted with antibodies to cell-membrane proteins. Depending on the coverage of the functional groups, we predict two distinct regimes. In the low coverage localized regime, there is an exponential distribution of departure times. As the coverage is increased the system enters a diffusive regime resulting from the interplay of particle desorption and diffusion. This interplay leads to much longer bound state lifetimes, a phenomenon qualitatively similar to aging in glassy systems. The diffusion behavior is analogous to dispersive transport in disordered semiconductors: depending on the interaction parameters it may range from a finite renormalization of the diffusion coefficient to anomalous, subdiffusive behavior. We make connections to recent experiments and discuss the implications for future studies.

cond-mat.soft↗

Effects of Sequence Disorder on DNA Looping and Cyclization

Effects of sequence disorder on looping and cyclization of the double-stranded DNA are studied theoretically. Both random intrinsic curvature and inhomogeneous bending rigidity are found to result in a remarkably wide distribution of cyclization probabilities. For short DNA segments, the range of the distribution reaches several orders of magnitude for even completely random sequences. The ensemble averaged values of the cyclization probability are also calculated, and the connection to the recent experiments is discussed.

cond-mat.soft↗

Role of boundary constraints in DNA cyclization

We modify the classical Shimada-Yamakawa theory of DNA looping by generalizing the form of boundary constraints. This generalization is important in the context of DNA cyclization experiments since it mimics the reduced local rigidity of the "nicked" DNA loop. Our results indicate that the non-trivial boundary constraints may be responsible for the existing dramatic discrepancy between various DNA cyclization experiments. The developed effective Hamiltonian method may be further extended to a broad class of DNA looping problems.

q-bio.BM↗

Elasticity of strongly stretched ssDNA

We present a simple model which describes elastic response of single-stranded DNA (ssDNA) to stretching, including the regime of very high force (up to 1000 pN). ssDNA is modelled as a discreet persistent chain, whose ground state is a zigzag rather than a straight line configuration. This mimics the underlying molecular architecture and helps to explain the experimentally observed staturation of the stretching curve at very high force.

q-bio.BM↗

Self-assembly of DNA-coded nanoclusters

We present a theoretical discussion of a self-assembly scheme which makes it possible to use DNA to uniquely encode the composition and structure of micro- and nanoparticle clusters. These anisotropic DNA-decorated clusters can be further used as building blocks for hierarchical self-assembly of larger structures. We address several important aspects of possible experimental implementation of the proposed scheme: the competition between different types of clusters in a solution, possible jamming in an unwanted configuration, and the degeneracy due to symmetry with respect to particle permutations.

cond-mat.soft↗