Papers by Anatoly Kolomeisky
The Journal of Physical Chemistry C, 2009
Recent single-molecule experiments indicated that thioethers (dialkyl sulfides) on gold surfaces ... more Recent single-molecule experiments indicated that thioethers (dialkyl sulfides) on gold surfaces act as thermallyor mechanically activated molecular rotors, although the mechanisms for these phenomena are not yet clearly understood. Here we present theoretical and experimental investigations of the rotational dynamics of these thioether molecules. Single-molecule studies utilizing low-temperature scanning tunneling microscopy allowed us to determine rotational rates and activation energies for the rotation of symmetric dialkyl sulfides. It was found that the rotational energy barriers increased as a function of alkyl chain length but then quickly saturated. Molecular dynamics simulations have also been performed in order to understand the molecular rotations of thioethers, and our theoretical calculations agree well with experimental observations. It is argued that the observed rotational dynamics of dialkyl sulfides are determined by the effective interactions with the surface and the flexibility of the alkyl chains. These results suggest possible ways to control and utilize thioether rotors at the single-molecule level.
APS Meeting Abstracts, Jan 1, 2008
Asymmetric exclusion processes for particles moving on parallel channels with inhomogeneous coupl... more Asymmetric exclusion processes for particles moving on parallel channels with inhomogeneous coupling are investigated theoretically. Particles interact with hard-core exclusion and move in the same direction on both lattices, while transitions between the channels is allowed ...
The Journal of Physical Chemistry C, 2014
ABSTRACT The effect of morphology on singlet fission (SF) efficiency was investigated by using a ... more ABSTRACT The effect of morphology on singlet fission (SF) efficiency was investigated by using a combination of high-level electronic structure methods and a simple three-state kinetic model. The calculations reproduce the observed differences in SF efficiency in different polymorphs of 1,3-diphenylisobenzofuran (DPBF) and 1,6-diphenyl-1,3,5-hexatriene (DPH), as well as make predictions about 5,12-diphenyltetracene (DPT). The analysis of different factors contributing to the rates reveals that (i) there is more than one pair of adjacent chromophores that contribute to SF; (ii) not only slip-stacked configurations show efficient fission; and (iii) both electronic couplings and energy differences are responsible for different rates. The model predicts that the difference in SF efficiency in DPBF and DPH polymorphs increases at low temperature. In contrast, temperature dependence of the relative rates in the two DPT forms is predicted to be small. Our model predicts similar rates for the two polymorphs of DPT, although one form features much more favorable electronic couplings. This prediction depends strongly on the magnitude of Davydov's splitting; small changes in its value may change the ratio in favor of faster SF in xylene-grown crystals of DPT.
The Journal of Physical Chemistry C, 2014
A simple three-state model for the dynamics of the singlet fission (SF) process is developed. The... more A simple three-state model for the dynamics of the singlet fission (SF) process is developed. The model facilitates the analysis of the relative significance of different factors, such as electronic energies, couplings, and the entropic contributions. The entropic contributions to the rates are important; they drive the SF process in endoergic cases (such as tetracene). The anticipated magnitude of entropic contributions is illustrated by simple calculations. By considering a series of three acenes (tetracene, pentacene, and hexacene), we explained the experimentally observed 3 orders of magnitude difference in the rate of SF in tetracene and pentacene and predicted that the rate in hexacene will be slightly faster than in pentacene. This trend is driven by the increased thermodynamic drive for SF (Gibbs free energy difference of the initial excitonic state and two separated triplets). The model also explains experimentally observed fast SF in 5,12diphenyltetracene. Consistently with the experimental observations, the model predicts weak temperature dependence of the multiexciton formation rate in tetracene as well as a reduced rate of this step in solutions and in isolated dimers.
The Journal of Physical Chemistry C, 2009
Recent single-molecule experiments indicated that thioethers (dialkyl sulfides) on gold surfaces ... more Recent single-molecule experiments indicated that thioethers (dialkyl sulfides) on gold surfaces act as thermallyor mechanically activated molecular rotors, although the mechanisms for these phenomena are not yet clearly understood. Here we present theoretical and experimental investigations of the rotational dynamics of these thioether molecules. Single-molecule studies utilizing low-temperature scanning tunneling microscopy allowed us to determine rotational rates and activation energies for the rotation of symmetric dialkyl sulfides. It was found that the rotational energy barriers increased as a function of alkyl chain length but then quickly saturated. Molecular dynamics simulations have also been performed in order to understand the molecular rotations of thioethers, and our theoretical calculations agree well with experimental observations. It is argued that the observed rotational dynamics of dialkyl sulfides are determined by the effective interactions with the surface and the flexibility of the alkyl chains. These results suggest possible ways to control and utilize thioether rotors at the single-molecule level.
The Journal of Chemical Physics, 2013
The dynamics of translocation of polymer molecules through nanopores is investigated via molecula... more The dynamics of translocation of polymer molecules through nanopores is investigated via molecular dynamics. We find that an off-lattice minimalist model of the system is sufficient to reproduce quantitatively all the experimentally observed trends and scaling behavior. Specifically, simulations show (i) two translocation regimes depending on the ratio of pore and polymer length, (ii) two different regimes for the probability of translocation depending on applied voltage, (iii) an exponential dependence of translocation velocity upon applied voltage, and (iv) an exponential decrease of the translocation time with temperature. We also propose a simple theoretical explanation of each of the observed trends within a free energy landscape framework.
Biophysical Journal, 2015
The inducible transcription factor Egr-1, which recognizes a 9-bp target DNA sequence via three z... more The inducible transcription factor Egr-1, which recognizes a 9-bp target DNA sequence via three zincfinger domains, rapidly activates particular genes upon cellular stimuli such as neuronal signals and vascular stresses. Here, using the stopped-flow fluorescence method, we measured the target search kinetics of the Egr-1 zinc-finger protein at various ionic strengths between 40 and 400 mM KCl and found the most efficient search at 150 mM KCl. We further investigated the kinetics of intersegment transfer, dissociation, and sliding of this protein on DNA at distinct concentrations of KCl. Our data suggest that Egr-1's kinetic properties are well suited for efficient scanning of chromosomal DNA in vivo. Based on a newly developed theory, we analyzed the origin of the optimal search efficiency at physiological ionic strength. Target association is accelerated by nonspecific binding to nearby sites and subsequent sliding to the target as well as by intersegment transfer. Although these effects are stronger at lower ionic strengths, such conditions also favor trapping of the protein at distant nonspecific sites, decelerating the target association. Our data demonstrate that Egr-1 achieves the optimal search at physiological ionic strength through a compromise between the positive and negative impacts of nonspecific interactions with DNA.
Dynamic properties of molecular motors whose motion is powered by interactions with specific latt... more Dynamic properties of molecular motors whose motion is powered by interactions with specific lattice bonds are studied theoretically with the help of discrete-state stochastic "burnt-bridge" models. Molecular motors are depicted as random walkers that can destroy or rebuild periodically distributed weak connections ("bridges") when crossing them, with probabilities $p_1$ and $p_2$ correspondingly. Dynamic properties, such as velocities and dispersions, are
Condensed Matter Physics, 2010
Dynamic properties of molecular motors whose motion is powered by interactions with specific latt... more Dynamic properties of molecular motors whose motion is powered by interactions with specific lattice bonds are studied theoretically with the help of discrete-state stochastic "burnt-bridge" models. Molecular motors are depicted as random walkers that can destroy or rebuild periodically distributed weak connections ("bridges") when crossing them, with probabilities p 1 and p 2 correspondingly. Dynamic properties, such as velocities and dispersions, are obtained in exact and explicit form for arbitrary values of parameters p 1 and p 2 . For the unbiased random walker, reversible burning of the bridges results in a biased directed motion with a dynamic transition observed at very small concentrations of bridges. In the case of backward biased molecular motor its backward velocity is reduced and a reversal of the direction of motion is observed for some range of parameters. It is also found that the dispersion demonstrates a complex, non-monotonic behavior with large fluctuations for some set of parameters. Complex dynamics of the system is discussed by analyzing the behavior of the molecular motors near burned bridges.
Nucleic acids research, 2014
The inducible transcription factor Egr-1, which recognizes a 9-bp target DNA sequence via three z... more The inducible transcription factor Egr-1, which recognizes a 9-bp target DNA sequence via three zinc-finger domains, rapidly activates particular genes upon cellular stimuli such as neuronal signals and vascular stresses. Here, using the stopped-flow fluorescence method, we measured the target search kinetics of the Egr-1 zinc-finger protein at various ionic strengths between 40 and 400 mM KCl and found the most efficient search at 150 mM KCl. We further investigated the kinetics of intersegment transfer, dissociation, and sliding of this protein on DNA at distinct concentrations of KCl. Our data suggest that Egr-1's kinetic properties are well suited for efficient scanning of chromosomal DNA in vivo. Based on a newly developed theory, we analyzed the origin of the optimal search efficiency at physiological ionic strength. Target association is accelerated by nonspecific binding to nearby sites and subsequent sliding to the target as well as by intersegment transfer. Although th...
Integrative biology : quantitative biosciences from nano to macro, 2013
Cancer cells become mobile by remodelling their cytoskeleton to form migratory structures. This t... more Cancer cells become mobile by remodelling their cytoskeleton to form migratory structures. This transformation is dominated by actin assembly and disassembly (polymerisation and depolymerisation) in the cytoplasm. Synthesis of filamentous actin produces a force at the leading edge that pushes the plasma membrane forward. We describe an assay to measure the restoring force of the membrane in response to forces generated within the cytoplasm adjacent to the membrane. A laser trap is used to form a long membrane nanotube from a living cell and to measure the axial membrane force at the end of the tube. When the tube, resembling a filopodium, is formed and in a relaxed state the axial membrane force exhibits a positive stationary value. This value reflects the influence of the cytoskeleton that acts to pull the tube back to the cell. A dynamic sawtooth force that rides upon the stationary value is also observed. This force is sensitive to a toxin that affects actin assembly and disassem...
Cellular and Molecular Bioengineering, 2012
Intracellular transport is a fundamental biological process during which cellular materials are d... more Intracellular transport is a fundamental biological process during which cellular materials are driven by enzymatic molecules called motor proteins. Recent optical trapping experiments and theoretical analysis have uncovered many features of cargo transport by multiple kinesin motor protein molecules under applied loads. These studies suggest that kinesins cooperate negatively under typical transport conditions, although some productive cooperation could be achieved under higher applied loads. However, the microscopic origins of this complex behavior are still not well understood. Using a discrete-state stochastic approach we analyze factors that affect the cooperativity among kinesin motors during cargo transport. Kinesin cooperation is shown to be largely unaffected by the structural and mechanical parameters of a multiple motor complex connected to a cargo, but much more sensitive to biochemical parameters affecting motor-filament affinities. While such behavior suggests the net negative cooperative responses of kinesins will persist across a relatively wide range of cargo types, it is also shown that the rates with which cargo velocities relax in time upon force perturbations are influenced by structural factors that affect the free energies of and load distributions within a multiple kinesin complex. The implications of these later results on transport phenomena where loads change temporally, as in the case of bidirectional transport, are discussed.
Shown below are the results from a comparison of fully methylated and unmethylated versions of th... more Shown below are the results from a comparison of fully methylated and unmethylated versions of the BRCA1 and MS3 genomic DNA fragments(A). Using quantitative PCR, we measured the number of DNA molecules which translocated through a 1.8nm nanopore at a given voltage(B). Unmethylated MS3 and BRCA1 translocate above 3.77V and 3.61V, respectively while the thresholds for fully methylated MS3 and BRCA1 are 2.53V and 2.69V respectively.
Scientific reports, 2014
This paper studies a weakly and asymmetrically coupled three-lane driven diffusive system. A non-... more This paper studies a weakly and asymmetrically coupled three-lane driven diffusive system. A non-monotonically changing density profile in the middle lane has been observed. When the extreme value of the density profile reaches ρ = 0.5, a bulk induced phase transition occurs which exhibits a shock and a continuously and smoothly decreasing density profile which crosses ρ = 0.5 upstream or downstream of the shock. The existence of double shocks has also been observed. A mean-field approach has been used to interpret the numerical results obtained by Monte Carlo simulations. The current minimization principle has excluded the occurrence of two or more bulk induced shocks in the general case of nonzero lane changing rates.
The journal of physical chemistry. B, Jan 13, 2015
Microtubules and actin filaments are biopolymer molecules that are major components of cytoskelet... more Microtubules and actin filaments are biopolymer molecules that are major components of cytoskeleton networks in biological cells. They play important roles in supporting fundamental cellular processes such as cell division, signalling, locomotion and intracellular transport. In cells cytoskeleton proteins function under nonequilibrium conditions that are powered by hydrolysis of adenosine triphosphate (ATP) or guanosine triphosphate (GTP) molecules attached to them. Although these biopolymers are critically important for all cellular processes, the mechanisms that govern their complex dynamics and force generation remain not well explained. One of the most difficult fundamental issues is to understand how different components of cytoskeleton proteins interact together. We develop an approximate theoretical approach for analyzing complex processes in cytoskeleton proteins that takes into account the multifilament structure, lateral interactions between parallel protofilaments, and th...
The Journal of chemical physics, Jan 14, 2014
Analysis of complex networks has been widely used as a powerful tool for investigating various ph... more Analysis of complex networks has been widely used as a powerful tool for investigating various physical, chemical, and biological processes. To understand the emergent properties of these complex systems, one of the most basic issues is to determine the structure and topology of the underlying networks. Recently, a new theoretical approach based on first-passage analysis has been developed for investigating the relationship between structure and dynamic properties for network systems with exponential dwell time distributions. However, many real phenomena involve transitions with non-exponential waiting times. We extend the first-passage method to uncover the structure of distinct pathways in complex networks with non-exponential dwell time distributions. It is found that the analysis of early time dynamics provides explicit information on the length of the pathways associated to their dynamic properties. It reveals a universal relationship that we have condensed in one general equat...
The journal of physical chemistry. B, Jan 4, 2014
Most chemical and biological processes can be viewed as reaction networks in which different path... more Most chemical and biological processes can be viewed as reaction networks in which different pathways often compete kinetically for transformation of substrates into products. An enzymatic process is an example of such phenomena when biological catalysts create new routes for chemical reactions to proceed. It is typically assumed that the general process of product formation is governed by the pathway with the fastest kinetics at all time scales. In contrast to the expectation, here we show theoretically that at time scales sufficiently short, reactions are predominantly determined by the shortest pathway (in the number of intermediate states), regardless of the average turnover time associated with each pathway. This universal phenomenon is demonstrated by an explicit calculation for a system with two competing reversible (or irreversible) pathways. The time scales that characterize this regime and its relevance for single-molecule experimental studies are also discussed.
The journal of physical chemistry. B, Jan 23, 2014
We directly measure the dynamics of the HIV trans-activation response (TAR)-DNA hairpin with mult... more We directly measure the dynamics of the HIV trans-activation response (TAR)-DNA hairpin with multiple loops using single-molecule Förster resonance energy transfer (smFRET) methods. Multiple FRET states are identified that correspond to intermediate melting states of the hairpin. The stability of each intermediate state is calculated from the smFRET data. The results indicate that hairpin unfolding obeys a "fraying and peeling" mechanism, and evidence for the collapse of the ends of the hairpin during folding is observed. These results suggest a possible biological function for hairpin loops serving as additional fraying centers to increase unfolding rates in otherwise stable systems. The experimental and analytical approaches developed in this article provide useful tools for studying the mechanism of multistate DNA hairpin dynamics and of other general systems with multiple parallel pathways of chemical reactions.
The Journal of chemical physics, Jan 14, 2014
Complex Markov models are widely used and powerful predictive tools to analyze stochastic biochem... more Complex Markov models are widely used and powerful predictive tools to analyze stochastic biochemical processes. However, when the network of states is unknown, it is necessary to extract information from the data to partially build the network and estimate the values of the rates. The short-time behavior of the first-passage time distributions between two states in linear chains has been shown recently to behave as a power of time with an exponent equal to the number of intermediate states. For a general Markov model we derive the complete Taylor expansion of the first-passage time distribution between two arbitrary states. By combining algebraic methods and graph theory approaches it is shown that the first term of the Taylor expansion is determined by the shortest path from the initial state to the final state. When this path is unique, we prove that the coefficient of the first term can be written in terms of the product of the transition rates along the path. It is argued that ...
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Papers by Anatoly Kolomeisky