Dr. Akhremitchev research interests are in experimental biophysical chemistry and physical chemistry. Biophysical research focuses on understanding the physico-chemical mechanisms of the initial stages of amyloid fibril formation. Optical and scanning probe techniques are employed to investigate the conformational dynamics and intermolecular interactions of disease-related proteins. Research in physical chemistry concentrates on quantifying the energy landscape parameters of hydrophobic interactions. This research further develops the single-molecule dynamic force spectroscopy to uncover information that is not available by other techniques. Of the related interest is the examination of the systematic errors in force spectroscopy that offset the resulting values of the energy landscape parameters.
We have three major areas of research. (1) Surface Chemistry. We also devote a substantial effort to the attachment chemistry and array fabrication chemistry strategies for oligonucleotides (both DNA and RNA), polypeptides, proteins, and carbohydrates at chemically modified gold surfaces. Our attachment chemistry utilizes linking reactions of modified biomolecules with self assembled of alkanethiol monolayers. We have also created some unique microfluidic methods for creating biopolymer arrays. (2) Surface Spectroscopy. We rely on a variety of surface sensitive spectroscopies to characterize condensed phase interfaces. For example, we routinely use Polarization Modulation FTIR Reflection-Absorption Spectroscopy (PM-FTIRRAS) to obtain the infrared vibrational spectra of ultrathin organic films at metal surfaces. Our PM-FTIR experiments are performed with the Synchronous Sampling Demodulator (SSD) electronics from GWC Technologies. Another area that we've been working in for a number of years is the application of optical spectroscopies such as the nonlinear optical technique of Second Harmonic Generation (SHG) to the study of surfactants at liquid/liquid interfaces,including the interface between two immiscible electrolyte solutions. Most recently, we've been working on the development of ultrathin polypeptide films for the study of liquid/liquid interfaces. Most recently, we have been using surface plasmon resonance imaging (SPR imaging) measurements to optically detect bioaffinity binding events at gold surfaces. (3) Surface Biochemistry. SPR Imaging Measurements of Biopolymer Adsorption. A significant portion of our research is devoted to the use of Surface Plasmon Resonance (SPR) as a method for monitoring the adsorption of molecules onto chemically modified gold surfaces. Some of our most recent efforts have been in the study of the adsorption of biopolymers such as oligonucleotides and proteins.
Prof. Nancy Forde's research interests involve: Mechanical properties of single molecules, Protein folding, Materials design, and Technique development of Optical tweezers and Magnetic tweezers. Mechanical experiments on single molecules can provide a wealth of information on the response of systems to an applied force under both equilibrium and nonequilibrium conditions, enabling not only a description of the average mechanical properties but also providing additional information that can be obtained from the underlying distribution. Studying the pathway by which a protein unfolds when subjected to externally applied force provides insight into the folding/unfolding pathway complementary to that available from bulk techniques, allowing us to see if there is a unique pathway to attaining its three-dimensional form. How much do the mechanical properties of individual molecules contribute to the mechanical response of a higher-order system? We can systematically add increasing complexity to the systems we characterize, for example by including intermolecular interactions, in order to gain insight into the separability of simple and higher-order effects. By developing an understanding of the molecular basis for mechanical response, we can thus start to rationally design materials with desired physical properties.
When studying the dynamics of solute molecules in the condensed phase using molecular dynamics, the need to simulate the motions of many solvent molecules often limits the type of system that can be investigated. Research in this area is concerned with the construction of mesoscopic models for molecular dynamics that allow one to bridge space and time scales and simulate large complex systems. Applications to nano-clusters, reactive processes and biomolecule dynamics in solution are being carried out.The macroscopic dynamics of systems constrained to lie far from equilibrium can be very rich, ranging from simple steady states to complex oscillatory or chaotic motion. Physical systems of this type are common in nature and the observed phenomena include fluid and chemical turbulence, instabilities in lasers and nonlinear optical devices and periodic and aperiodic behaviour in biological systems like the heart and nerve tissue. Chemical systems provide good examples for the study of such phenomena. One of the main thrusts of current research in this area in the interplay between space and time in nonlinear dynamical systems. A variety of techniques in nonlinear dynamical systems theory are being applied to the study of macroscopic and microscopic models for dynamics of these systems.
The goal of our research in drug, peptide/protein, and gene delivery is to establish novel concepts and unique designs for carriers having a polymeric nature, focusing on nanoscopic delivery systems. We research physical/chemical assembly, stable integration of bioactive elements, and detailed structure-property relationships for drug delivery. This thrust of research relies on creative efforts in polymer chemistry, a detailed understanding of physicochemical properties of polymers and associated drugs, and deep insight into drug action and disease, a critical requirement for the prediction of events in vivo and advancement of drug delivery, drug targeting, and ultimately therapy. We are interested in polymeric micelles as nanoscopic delivery systems, seeking an understanding of structure-property relationships for drug solubilization, controlled release, and drug targeting. Recent research efforts focus on combination drug delivery for the treatment of life-threatening systemic fungal diseases and cancer, aiming for synergistic drug effects, achieved from a genuine appreciation for drug action. This thrust of our research takes advantage of good compatibility and unique stability of polymeric micelles in water, carrying different solubilized drugs. The concept of mixed polymeric micelle-drug conjugates, bearing more than one kind of drug is also being explored, trying to understand physical stability after assembly (Janus micelle?), triggered drug release in response to pH changes, pharmacokinetics (identical on a macroscopic or cellular level?), and drug activity in cell culture experiments and murine models of disease.
Brain structure and function can be mapped using a variety of non-invasive magnetic resonance methodologies. Functional MRI (fMRI) is used to identify areas of brain function, magnetic resonance spectroscopy (MRS) shows metabolic information, and diffusion tensor imaging (DTI) provides detailed strutural maps. In my lab we are using a combination of these techniques to study normal and diseased human brain and muscle. Methods to evaluation tissue microvasculature, particularly perfusion, blood volme, and capillary permeability, are being developed using MRI contrast agent approaches and perfusion sensitive MRI methods. Additionally we are developing new imaging pulse sequence methods and rf imaging coils for use with these studies. Current projects include: 1. analysis of microcirculation using correlative magnetic resonance imaging and analytical electron microscopy; 2. evaluation of physiologically induced BOLD signal heterogeneity; 3. functional MRI and diffusion imaging using parallel processing; 4. in vivo 1H/31P spectroscopy with tailored rf pulses; 5. perfusion using contrast agent and non-contrast agent approaches.
The overall focus of our research has been on the biological interactions which are central to the control of biological function; attempting to relate protein structure, kinetics, dynamics, and thermodynamics to function.
Heart disease is the leading cause of death in western society for men and women. The long term focus of our program is the elucidation of the molecular details of the calcium mediated thin filament based regulation of contraction in cardiac and skeletal muscle. Recent discoveries have seen a great expansion in the number of sacromere proteins, concomitant appreciation of the interconnected cytoskeletal network critical for contractile activity, and a recognition of a large number of mutations in these cytoskeletal components which account for a number of human myopathies. Of special medical importance because of the prevalence of cardiovascular disease are the cardiac regulatory proteins, where phosphorylation of cardiac troponin plays a major role in mediating myofilament physiology; troponin mutations are implicated in various cardiac diseases including familial hypertrophic cardiomyopathy which are amongst the most frequently occurring inherited cardiac disorders; troponin proteins are important markers of cardiovascular damage; and cardiac troponin is subject to influence by cardiotonic drugs, which may be used to modulate the calcium response of the myofilaments in diseased hearts. Thus, there is a strong interest and need in understanding the structure and dynamics of these proteins.
Most of our research involves the determination of the solution structure and dynamics of muscle proteins using high field, multinuclear, multidimension Nuclear Magnetic Resonance spectroscopic techiques. We are also developing new solid state NMR techniques for the determination of the orientation and in situ structures of the thin filament regulatory proteins in intact muscle fibers. This will allow us to connect high resolution structural and dynamic changes to physiological and functional measurements (i.e., force).
Our task is to investigate how synthetic biochemical systems can be designed to carry out algorithms and compute; what models of computation arise from biochemical processes and how they can be programmed; and how to "compile" abstract descriptions of biomolecular algorithms down to specific synthetic DNA sequences that implement the desired computation in the laboratory.
Like the carefully orchestrated molecular processes that occur within living cells, biomolecular computation can in principle occur autonomously, without the need for any external intervention during the computation. Being able to design and understand such systems is our ultimate goal. We are exploring several interconnected paradigms of biomolecular computation, based loosely on processes that are ubiquitous throughout living organisms:
Algorithmic self-assembly of DNA tiles encodes information in the geometric arrangement of tiles, and performs logical steps by the selective addition of tiles as geometrically compatible sites.
In vitro RNA transcriptional circuits are a stripped-down, bare-bones version of genetic regulatory networks in the cell; signals are carried by the concentration of specific RNA transcripts; RNA polymerase and RNase regulate the production and degradation of RNA.
Biochemical circuits, such as cellular signal transduction cascades, are logically related to boolean circuits.
Chemical self-replication and evolution must have gotten started somehow, way back when. they are using algorithmic self-assembly to investigate a radical hypothesis of Graham Cairns-Smith, that life got started as clay crystals that reproduced patterns as they grew.
RNA and DNA hybridization and folding are essential processes for all DNA computing, and can perform complex logical operations in their own right.