Yuri Berlin

• Ph. D., Research Professor
• Professor at Northwestern University

DNA-based molecular electronics will require charges to be transported from one site within a 2D or 3D architecture to another. While this has been shown previously in linear, π-stacked DNA sequences, the dynamics and efficiency of charge transport across a DNA three-way junction (3WJ) have yet to be determined. Here, we present an investigation of...

A model for the low bias electric conductance of junctions consisting of a thin organic film (TOF) positioned between two metallic electrodes (M) has been developed. In contrast with other theoretical studies, the proposed model relies on the energy band picture of M-TOF-M systems. Theoretical analysis of the band-like transport has shown that the...

The coherent hole transfer in three types of DNA hairpins containing strands with adenine (A) and guanine (G) nucleobases has been studied. The investigated hairpins involve A n+1 GGA n , A n GAGA n , or (AG) 2n A strands that connect the hole donor and hole acceptor located on opposite ends of hairpins. The positive charge transfer from the photo-...

Charge transport through the DNA double helix is of fundamental interest in chemistry and biochemistry, but also has potential technological applications such as for DNA-based nanoelectronics. For the latter, it is of considerable interest to explore ways to influence or enhance charge transfer. In this Article we demonstrate a new mechanism for DN...

Molecular structures that direct charge transport in two or three dimensions could help to enable the development of molecule-based electrical switches and gates. As a step toward this goal, we use theory, modeling and simulation to explore DNA three-way junctions (TWJs). Molecular dynamics simulations and quantum calculations, indicate that DNA TW...

Numerical studies of hole migration along short DNA hairpins were performed with a particular emphasis on the variations of the rate and quantum yield of the charge separation process with the location of a single guanine:cytosine (G:C) base pair. Our calculations show that the hole arrival rate increases as the position of the guanine:cytosine bas...

We developed a model for hole migration along relatively short DNA hairpins with fewer that seven adenine (A):thymine (T) base pairs. The model was used to simulate hole migration along poly(A)-poly(T) sequences with a particular emphasis on the impact of partial hole localization on the different rate processes. The simulations, performed within t...

We developed a model for hole migration along relatively short DNA hairpins with fewer that seven adenine (A):thymine (T) base pairs. The model was used to simulate hole migration along poly(A)-poly(T) sequences with a particular emphasis on the impact of partial hole localization on the different rate processes. The simulations, performed within t...

We report a computational search for DNA π-stack structures exhibiting high electric conductance in the hopping regime, based on the INDO/S calculations of electronic coupling and the method of data analysis called k-means clustering. Using homogeneous poly(G)-poly(C) and poly(A)-poly(T) stacks as the simplest structural models, we identify the con...

I nterest in using deoxyribonucleic acid (DNA) as a building block for nanoelec-tronic devices originates from two im-portant properties of this molecule. One property is the ability of DNA to be orga-nized into predictable nanometer-sized structures in both two and three dimen-sions. This remarkable feature has been exploited to obtain a variety o...

Transfer of the electronic excitation energy in calf thymus DNA is studied by time-resolved fluorescence spectroscopy. The fluorescence anisotropy, after an initial decay starting on the femtosecond time scale, dwindles down to ca. 0.1. The in-plane depolarized fluorescence decays are described by a stretched exponential law. Our observations are c...

Charge migration is a ubiquitous phenomenon with profound implications throughout many areas of chemistry, physics, biology and materials science. The long-term vision of designing functional materials with tailored molecular scale properties has triggered an increasing quest to identify prototypical systems where truly molecular conduction pathway...

Donor-bridge-acceptor (D-B-A) systems in which a 3,5-dimethyl-4-(9-anthracenyl)julolidine (DMJ-An) chromophore and a naphthalene-1,8:4,5-bis(dicarboximide) (NI) acceptor are linked by oligomeric 2,7-fluorenone (FN(n)) bridges (n = 1-3) have been synthesized. Selective photoexcitation of DMJ-An quantitatively produces DMJ(+•)-An(-•), and An(-•) acts...

I nterest in using deoxyribonucleic acid (DNA) as a building block for nanoelec-tronic devices originates from two im-portant properties of this molecule. One property is the ability of DNA to be orga-nized into predictable nanometer-sized structures in both two and three dimen-sions. This remarkable feature has been exploited to obtain a variety o...

DNA hairpin conjugates with a stilbenedicarboxamide (Sa) hole donor and a stilbenediether (Sd) hole acceptor are considered as model systems for studying charge recombination (CR) of excess charges in DNA. Using the method of thermodynamic integration, we estimated the relative free energies of this process in hairpins with three adenine:thymine pa...

To decide whether counterions can affect the rate of charge recombination in DNA hairpins, the influence of the salt concentration on the free energy of this process was studied computationally using molecular dynamics simulations. The calculations were performed using the implicit treatment of the surroundings (the MM-PBSA and MM-GBSA techniques)...

Using a tight-binding model of charge transport in systems with static and dynamic disorder, we present a theoretical study of the positive charge transfer in molecular assemblies that involve a hole donor and an acceptor connected by fluorene and phenyl bridges. Two parameters that determine the rate of charge transfer within the proposed model ar...

To decide whether counterions can affect the rate of charge recombination in DNA hairpins, the influence of the salt concentration on the free energy of this process was studied computationally using molecular dynamics simulations. The calculations were performed using the implicit treatment of the surroundings (the MM-PBSA and MM-GBSA techniques)...

Using a tight-binding model of charge transport in systems with static and dynamic disorder, we present a theoretical study of the positive charge transfer in molecular assemblies that involve a hole donor and an acceptor connected by fluorene and phenyl bridges. Two parameters that determine the rate of charge transfer within the proposed model ar...

Over the past decade, the efficiency and mechanism of charge transfer in DNA have received a lot of attention from both experimentalists and theoreticians. 1-4 Apart from possible biologi-cal implications related to oxidative damage in DNA, it is a subject of considerable fundamental interest. DNA presents an excellent model for the study of charge...

DNA hairpins in which an electron donor and an electron acceptor are attached to the ends are excellent model systems for the study of charge transfer in weakly coupled pi-stacked systems. In this communication we report on a computational study of the effect of the base pair sequence in these DNA hairpins on the kinetics of charge transfer. We sho...

The influence of static and dynamic torsional disorder on the kinetics of charge transfer (CT) in donor-bridge-acceptor (D-B-A) systems has been investigated theoretically using a simple tight-binding model. In such systems, variations of the torsion angle often give rise either to static changes in the magnitude of electronic coupling along the br...

We present a theoretical study of the positive charge transfer in stilbene-linked DNA hairpins containing only AT base pairs using a tight-binding model that includes a description of structural fluctuations. The parameters are the charge transfer integral between neighboring units and the site energies. Fluctuations in these parameters were studie...

We present a theoretical study of the positive charge transfer in stilbene-linked DNA hairpins containing only AT base pairs using a tight-binding model that includes a description of structural fluctuations. The parameters are the charge transfer integral between neighboring units and the site energies. Fluctuations in these parameters were studie...

In Chap. 3, Berlin and Ratner describe charge migration in DNA within a theoretical framework of a variable-range hopping model which has been successfully used to analyze steady-state measurements of the charge transfer efficiency for this molecule. According to the model proposed, the ability of DNA to serve as the medium for very long-range (up...

In this part of the review we describe aspects of the physics of proteins at low temperature as they are reflected in the spectra of individual pigment–protein complexes. The focus of this review is on the spectral diffusion of chromophores that are naturally embedded in light-harvesting complexes from purple bacteria. From the spectral diffusion b...

We discuss aspects of the physics of proteins at low temperature as they are reflected in highly resolved optical spectra of molecular probes. Typical probe molecules are heme-like dyes, aromatic amino acids, but also extended molecular aggregates in light harvesting complexes. We put emphasis on the interactions of the probe with its protein envir...

To decide whether counterions can affect the rate of charge recombination in DNA hairpins, the influence of the salt concentration on the free energy of this process was studied computationally using molecular dynamics simulations. The calculations were performed using the implicit treatment of the surroundings (the MM-PBSA and MM-GBSA techniques)...

Absolute rates of hole transfer between guanine nucleobases separated by one or two A:T base pairs in stilbenedicarboxamide-linked DNA hairpins were obtained by improved kinetic analysis of experimental data. The charge-transfer rates in four different DNA sequences were calculated using a density-functional-based tight-binding model and a semiclas...

The relation between intra-molecular electron transfer in the donor-bridge-acceptor system and zero-bias conductance of the same bridge in the metal–molecule–metal junction is analyzed for the sequential hopping regime of both processes. The electron transfer rate and molecular conductance are expressed in terms of rates characterizing each individ...

Absolute rates of hole transfer between guanine nucleobases separated by one or two A:T base pairs in stilbenedicarboxamide-linked DNA hairpins were obtained by improved kinetic analysis of experimental data. The charge-transfer rates in four different DNA sequences were calculated using a density-functional-based tight-binding model and a semiclas...

Charge motion within DNA stacks, probed by measurements of electric conductiv-ity and by time-resolved and steady-state damage yield measurements, is determined by a complex mixture of electronic effects, coupling to quantum and classical degrees of freedom of the atomic motions in the bath, and the effects of static and dynamic disorder. The re-su...

We present results of a hole burning study with thermal cycling and waiting time spectral diffusion experiments on a modified cytochrome - c protein in its native as well as in its denatured state. The experiments show features which seem to be characteristic for the protein state of matter and its associated dynamics at low temperature. The proper...

We present results of a hole burning study with thermal cycling and waiting time spectral diffusion experiments on a modified cytochrome ‐ c protein in its native as well as in its denatured state. The experiments show features which seem to be characteristic for the protein state of matter and its associated dynamics at low temperature. The proper...

We report calculations of solvent reorganization energies and the energy gap analysis for charge transfer in synthetic DNA hairpins consisting of two complementary strands linked by a stilbene chromophore. Reorganization energies are calculated for the processes of photoinduced hole injection from the linker to a neighboring guanine (G) through var...

Charge transport in molecular wires is investigated theoretically within the framework of a simple hopping model. The model suggests that each elementary hopping step can be treated as an electron-transfer reaction between ionic and neutral states of π-conjugated structural units coupled through σ-bonded spacers. Within this mechanistic picture, th...

Charge transport in molecular wires is investigated theoretically within the framework of a simple hopping model. The model suggests that each elementary hopping step can be treated as an electron-transfer reaction between ionic and neutral states of π-conjugated structural units coupled through σ-bonded spacers. Within this mechanistic picture, th...

Using stacks of Watson–Crick base pairs as an important example of multichromophoric molecular assemblies, we studied charge migration in DNA with special emphasis on the mechanism of hole hopping between neighboring guanines (G) connected by the adenine–thymine (AT) bridge. The tight-binding model proposed for this elementary step shows that for s...

Recently, it has become possible to measure the mobility of charges along isolated chains of conjugated polymers. The mobility of holes along poly(phenylenevinylene) and polythiophene backbones were reported to be 0.43 and 0.02 cm2 V-1 s-1, respectively. The large difference between the mobility of holes on poly(phenylenevinylene) and polythiophene...

Charge migration in DNA has been a subject of considerable debate over the last decade. The interior of DNA consist of a stack of aromatic hydrogen-bonded base pairs that resembles a one-dimensional π-conducting structure found in discotic materials (see graphic), but the structure of DNA is highly disordered and fluctuations occur on timescales of...

An anomalous power law behavior of spectral diffusion broadening of persistent holes is found in large biological molecules dissolved in a glassy host at very low temperature. We argue that this is caused by the internal degrees of freedom of the biomolecule itself rather than by excitations of the glassy host. To explain the observed universal tim...

The exact semiclassical wavefunction for a tunneling electron, coupled to the degrees of freedom of the host medium, is constructed. As a specific application, the result is used to calculate the tunneling amplitude for the electron interacting with a single vibrational mode of the medium. In agreement with previous numerical studies, the tunneling...

We develop an adiabatic hopping model for charge migration through molecules dissolved in a polar liquid (water), based on an analytical approach [1]. The charge hopping between donor and acceptor states is due to a rare fluctuation of the solvent polarization forming a deeper well at the target places. The results are applied to the photoexcited h...

KEYWORDS: ab initio calculations ¥ charge carrier mobility ¥ charge transfer ¥ DNA damage Charge migration in DNA is a subject of intense current study [1±13] partially motivated by various potential applications ranging from functional nanoscale electronic devices [14±16] to long-range detection of DNA damage. [17, 18] A key structural element, wh...

Recently, it has become possible to measure the mobility of charges along isolated chains of conjugated polymers. The mobility of holes along poly(phenylenevinylene) and polythiophene backbones were reported to be 0.43 and 0.02 cm 2 V -1 s -1 , respectively. The large difference between the mobility of holes on poly-(phenylenevinylene) and polythio...

The concept of gating has been applied to the theoretical description of rate processes coupled to conformational rearrangements of biological macromolecules both out of equilibrium and near equilibrium. The out-of-equilibrium rearrangements are discussed in terms of requirements imposed by the complexity of biomolecules. These include (i) a variet...

The exact semiclassical wave function for a tunneling electron, coupled to the degrees of freedom of a host medium, is constructed. This permits a description of electron dynamics within the barrier. As a specific application, the result is used to calculate the tunneling amplitude for the electron interacting with the single vibrational mode of th...

The efficiency of charge migration through stacked Watson-Crick base pairs is analyzed for coherent hole motion interrupted by localization on guanine (G) bases. Our analysis rests on recent experiments, which demonstrate the competition of hole hopping transitions between nearest neighbor G bases and a chemical reaction of the cation G(+) with wat...

The efficiency of charge migration through stacked Watson-Crick base pairs is analyzed for coherent hole motion interrupted by localization on guanine (G) bases. Our analysis rests on recent experiments, which demonstrate the competition of hole hopping transitions between nearest neighbor G bases and a chemical reaction of the cation G + with wate...

The use of the DNA duplex as a molecular wire is discussed with particular attention to recent experimental findings. Experimental studies of photo-excited hole dynamics in DNA can be understood within the phenomenological hopping model. However a microscopic first principles approach requires taking into account the interaction between charge and...

The efficiency of charge migration through stacked Watson-Crick base pairs is analyzed for coherent hole motion interrupted by localization on guanine (G) bases. Our analysis rests on recent experiments, which demonstrate the competition of hole hopping transitions between nearest neighbor G bases and a chemical reaction of the cation G + with wate...

A theory of electron motion over randomly situated centres is developed. The electron binding energy in the centres is assumed to be constant. By means of the concepts developed in percolation theory all the centres can be separated into two groups. The first group makes a diffusion cluster responsible for the macroscopic transport. The second grou...

In this work the mechanism of migration of positive charges through donor-DNA-acceptor systems is studied using a quantum mechanical model based on the tight-binding approximation. For DNA bridges containing only adenine-thymine (AT) base pairs the difference in ionization potential between the donor moiety and the AT base pairs (i.e., the injectio...

Physical mechanisms that might assure the functioning of DNA as a molecular wire are considered on the basis of recent progress in understanding long-range charge transfer in this biologically important molecule. Our analysis shows that DNA behaves as an insulator at low bias, while beyond the threshold the current sharply increases. Such behaviour...

Physical mechanisms that might assure the functioning of DNA as a molecular wire are considered on the basis of recent progress in understanding long-range charge transfer in this biologically important molecule. Our analysis shows that DNA behaves as an insula-tor at low bias, while beyond the threshold the current sharply increases. Such behaviou...

The sequence dependence of charge transport through stacked Watson-Crick base pairs was analyzed for coherent hole motion interrupted by a temporary charge localization on guanine bases. The relative rate of hole transfer to the GGG sequence has been expressed in terms of the frequency of jumps through adenine-thymine base pairs separating adjacent...

We have theoretically studied charge transfer in donor–DNA–acceptor systems by using a quantum mechanical model based on the tight-binding approach and by applying the Miller–Abrahams model of incoherent hopping model. According to the quantum mechanical model, the rate for charge transfer through DNA bridges consisting of adenine–thymine (AT) base...

The relation between the drift mobility and the diffusion coefficient of charge carriers in one-dimensional systems with energy disorder is investigated. By using the effective medium approximation, we derived expressions for these transport coefficients. The analytical results verified by computer simulations demonstrate that the Einstein relation...

The consideration of irreversible stochastic transitions (IST) in complex stochastic systems based on the most general probabilistic formalism is performed. The key quality, transition probability per unit time, alpha , is strictly introduced without referring to the conventional approach to the IST description. The expressions obtained for transit...

We have theoretically studied charge transfer in donorDNAacceptor systems by using a quantum mechanical model based on the tight-binding approach and by applying the MillerAbrahams model of incoherent hopping model. According to the quantum mechanical model, the rate for charge transfer through DNA bridges consisting Ž. of adeninethymine AT base pa...

We have measured the mobility of charge carriers along the one-dimensional conducting pathways provided by columnar stacks of triphenylene units in the liquid crystalline dimer 1,10-di-[3‘,6‘,7‘,10‘,11‘-pentabutyloxytriphenylenyl-2-oxy]decane using the pulse-radiolysis time-resolved microwave conductivity (PR-TRMC) and the time-of-flight (TOF) tech...

We have theoretically studied the competitive effects of static and dynamic energy disorder on the quantum-mechanical propagation of charge carriers and excitations along one-dimensional pathways consisting of coupled classical oscillators. Both the probability to survive in the initially occupied state and the propagation along the chain were inve...

The energy relaxation during thermally activated diffusion along one-dimensional chains with equally spaced traps of random energy depths has been studied both analytically and by computer simulations. Several time intervals, where the mean particle energy exhibits distinct temporal and temperature behaviors, have been identified. The explicit form...

Recent results on the computer simulations of thermally activated diffusion along one-dimensional chains with energetic disorder are analyzed theoretically. The analysis has enabled us to assign the numerical data to the particular stage of the diffusion process and to approximate the temporal behavior of the mean-square displacement during this st...

Reasoning from the correlation between the height of the reaction barrier and the energy depth of substates attributed to different configurations of the reactant surroundings, the phenomenological approach to the rate processes in complex media has been proposed. The approach allows the formulation of the model based exclusively on the energetic c...

A class of models has been proposed for the dynamics of the local configurational changes governing rate processes in complex systems. Models that fall into this class are based on a hierarchical picture of a complex object. In addition, they include constraints in order to take into account the coupling between local and global configurational rea...

The thermally activated diffusive motion in one-dimensional (1-d) disordered systems has been studied by using both an analytical method based on the effective medium approach and the Monte Carlo simulation method. The results obtained are used for proposing a procedure to construct approximate expressions for the 1-d diffusion coefficient valid in...

A theory of irreversible random transitions has been applied to rate processes coupled to configurational rearrangements of non-equilibrium complex systems. The rearrangements are discussed in terms of three main requirements imposed by the complexity of the object, i.e. the dynamic behavior of various degrees of freedom, constraints arising due to...

The problem of diffusion in one-dimensional disordered systems has been considered within the framework of the effective medium approximation. Several time intervals where the diffusion coefficient exhibits distinct temporal and temperature behaviors have been identified. The explicit forms of these dependences within each of the intervals are spec...

The "paradox of optical isomers" revealed by Hund in 1927 is re-examined taking into account the interaction of a chiral molecule with phonons of optically inactive solids below the Debye temperature / D. It has been shown, that in the strong coupling limit, where the dephasing rate is much higher than the energy splitting frequency, the interactio...

Fluctuations, static disorder and other external random impacts are known to be important factors affecting the mechanism and kinetics of chemical reactions in condensed media. Such randomly affected reactions are discussed here in the framework of the irreversible random transition theory and cover the entire range of physical conditions having an...

The dispersive transport model for relaxation of photolyzed heme proteins has been improved to take into account the coupling of the ligand-heme geminate recombination and the non-Gaussian diffusive dynamics of conformational changes in heme proteins. Contrary to the earlier deterministic version of the model, the present more rigorous formulation...

A general approach to the description of monomolecular reactions affected by random impacts has been developed on the basis of irreversible random transitions theory. Theoretical results derived allow us to account for concrete forms of stochastic affections and to evaluate statistical characteristics of reaction systems with monomolecular processe...

The percolation approach to the diffusion of charge carriers in disordered systems is applied to the analysis of their reactivity in the case, when the reaction rate is controlled by the dispersive transport of reactants. Expressions for quantities, which govern kinetics of both bulk and geminate elementary processes, have been derived. Our theoret...

A microscopic model for relaxation in the course of CO rebinding to heme proteins has been developed. The model demonstrates that above 170 K the barrier height for the ligand—heme geminate recombination increases with time non-exponentially and that the relaxation rate coefficient does not obey the Arrhenius law. These and some other theoretical f...

A problem of correlated fluctuations in multielement systems is considered in the framework of the theory of stochastic branching processes and is formulated in terms of a population model. Correlations have been taken into account by means of the heredity function. An explicit mathematical method is proposed to solve the problem without referring...

A new evolutionary model with hereditary modes considered as correlated fluctuations of fertility has been proposed. It has been demonstrated that the model allows the global statistical properties of the system to be evaluated, e.g. the ensemble average and the probability of extinction. The results obtained show the increase of instability of a p...

A new approach to treat the substates hierarchy in complex biochemical and physicochemical systems (such as spin glasses, proteins, various biological objects, etc.) is proposed. This approach introduces the possibility of taking into account energy-landscape fluctuations as well as correlations between the fluctuations in distinct scales and overl...

The expression for the apparent rate constant ka of partially diffusion-controlled reactions has been derived in the framework of the percolation approach to the description of the dispersive Gaussian transport of active species in disordered solids. Results obtained for site- and bond disordered systems agree with the empirical law ka = Bt−1+α and...

The behavior of the electron mobility in 2,2,4-trimethylpentane at high pressure is analyzed in the framework of the two-state model of electron transport. The increase in mobility at 22.5°, as the pressure increases, is shown to be correlated with an increase in μF, the free state mobility. The probability of localization first decreases slightly...

A theory of a geminate electron–cation recombination has been developed using the percolation approach to the description of the electron transport in disordered solids. Following this approach all trapping sites are separated into two groups. The first group forms a diffusion cluster responsible for the macroscopic charge transfer in disordered me...

Two interpretations of the parameter α are presented for a second-order equal-concentration kinetic equation with time-dependent reaction rate coefficient k(t) ∝tα−1, 0<α⩽1. The first, valid for any system, is in terms of the activation energy distribu for recombination and follows from the time dependence of the activation energy implied by the fo...

Carbon monoxide rebinding following laser photodissociation of carbon monoxy myoglobin in frozen solutions can be adequately described using the second-order equal concentration kinetic equation with a time-dependent rate constant deducible from the Kohlrausch relaxation function.

An earlier theory of thermal electron transport in liquid rare gases and saturated hydrocarbons yielded the radius of density fluctuations, A, as fitting parameters. Here, these data are rationalized in terms of a simple scattering model and thermodynamic density fluctuation. Assuming that the electron interacts with the same number of atoms, N, in...

An cartier theory of thermal electron transport in liquid rare gases and saturated hydrocarbons yielded the radius of density fluctuations, A, as fitting parameters. Here, these data are rationalized in terms of a simple scattering model and thermodynamic density fluctuation. Assuming that the electron interacts with the same number of atoms, N, in...

This paper studies the effect of HP on electrical conductivity of Pc and its metal complexes (NiPc, ZnPc, CoPc, CuPc). The Co, Ni, and ZnPc complexes were synthesized by known procedures, and the compounds were purified by repeated boiling with dilute aqueous HCI and NH/sub 4/OH. Extraction of impurities with hot methanol was performed until the ex...