Lawrence Livermore National Laboratory



Alexander Malkin

Senior Scientist
Biosciences and Biotechnology Division


 +1 925-423-7817


DegreeDiscipline/InstitutionYear
Ph.D. Chemistry
Institute of Crystallography, Russian Academy of Sciences, Moscow
1989
M.S. Chemistry
Moscow State University
1980

Research Interests

Biomaterials and Materials Science, Physics and Chemistry at the Interface, Theory and Practical Aspects of Crystallization and Self-Assembly, Biophysical Aspects of Microbial and Cellular Life Cycle, Bioforensics and Biological Sensors, Lignocellulosic Biomass Characterization and Biofuels, Assessment of Dual-Use Nanotechnologies, International Cooperative Threat Reduction, Probe Microscopy, Applications of High Resolution Imaging and Nanotechnology in Materials Science, Structural Biology, Biomass Conversion Technologies, Microbiology, and Medicine.

Publications

Over 80 peer-reviewed publications with over 3200 citations; Hirsch index: H = 37

Book and Book Chapters

J.J. DeYoreo, W. Casey, A.J. Malkin, E. Vlieg, M. Ward, Eds., (2001). Morphology and dynamics of crystal surfaces in complex molecular systems. Materials Research Society Symposium Proceedings, Vol. 620, Materials Research Society, Warrendale, PA.

A.J. Malkin (2011). Resolving the high-resolution architecture, assembly and functional repertoire of bacterial systems by in vitro atomic force microscopy. In: Life at the Nanoscale: Atomic Force Microscopy of Live Cells. (Ed. Y. Dufresne). Pan Stanford Publishing. Singapore, ISBN 978-981-4267-96-0, pp. 71-99.

A.J. Malkin and M.Plomp (2010). High-resolution architecture and structural dynamics of microbial and cellular system: Insights from high-resolution in vitro atomic force microscopy. In: Scanning Probe Microscopy of Functional Materials: Nanoscale Imaging and Spectroscopy. (Eds. S.V. Kalinin and A. Gruverman). Springer, New York, ISBN: 978-1-4419-6567-7, pp. 39-68.

A.J. Malkin, Yu.G. Kuznetsov, M.Plomp and A. McPherson (2008). Virus architecture probed by atomic force microscopy. In: Structure-based study of viral replication. (Eds. R.H. Cheng and T. Miayamura), World Scientific Pub Co., 289-310.

Research Interests

Biomaterials and Materials Science, Physics and Chemistry at the Interface, Theory and Practical Aspects of Crystallization and Self-Assembly, Biophysical Aspects of Microbial and Cellular Life Cycle, Bioforensics and Biological Sensors, Lignocellulosic Biomass Characterization and Biofuels, Assessment of Dual-Use Nanotechnologies, International Cooperative Threat Reduction, Probe Microscopy, Applications of High Resolution Imaging and Nanotechnology in Materials Science, Structural Biology, Biomass Conversion Technologies, Microbiology, and Medicine.

Publications

Over 80 peer-reviewed publications with over 3200 citations; Hirsch index: H = 34

Book and Book Chapters

J.J. DeYoreo, W. Casey, A.J. Malkin, E. Vlieg, M. Ward, Eds., (2001). Morphology and dynamics of crystal surfaces in complex molecular systems. Materials Research Society Symposium Proceedings, Vol. 620, Materials Research Society, Warrendale, PA.

A.J. Malkin (2011). Resolving the high-resolution architecture, assembly and functional repertoire of bacterial systems by in vitro atomic force microscopy. In: Life at the Nanoscale: Atomic Force Microscopy of Live Cells. (Ed. Y. Dufresne). Pan Stanford Publishing. Singapore, ISBN 978-981-4267-96-0, pp. 71-99.

A.J. Malkin and M.Plomp (2010). High-resolution architecture and structural dynamics of microbial and cellular system: Insights from high-resolution in vitro atomic force microscopy. In: Scanning Probe Microscopy of Functional Materials: Nanoscale Imaging and Spectroscopy. (Eds. S.V. Kalinin and A. Gruverman). Springer, New York, ISBN: 978-1-4419-6567-7, pp. 39-68.

A.J. Malkin, Yu.G. Kuznetsov, M.Plomp and A. McPherson (2008). Virus architecture probed by atomic force microscopy. In: Structure-based study of viral replication. (Eds. R.H. Cheng and T. Miayamura), World Scientific Pub Co., 289-310.

C. M. Schaldach, G. Bench, J. J. DeYoreo, T. Esposito, D. P. Fergenson, J. Ferreira, E. Gard, P. Grant, C. Hollars, J. Horn, T. Huser, M. Kashgarian, J. Knezovich, S. M. Lane, A. J. Malkin, M. Pitesky, C. Talley, H. J. Tobias, B. Woods, K-J. Wu, S. P. Velsko (2005). State of the art in characterizing threats: Non-DNA methods for biological signatures. In: Microbial Forensics. (Eds. S. Schutzer, R.G. Breeze, B. Budowle). New York, Elsevier Academic Press, 251-294.

A.J. Malkin, M. Plomp and A. McPherson (2005). Unraveling of the architecture of viruses by high-resolution atomic force microscopy. In: DNA Viruses: Methods and Protocols. (Ed. P.M. Lieberman), Methods in Molecular Biology Series. The Humana Press Inc., 85-108.

A.J. Malkin and R.E. Thorne (2004). Growth and disorder of macromolecular crystals: Insights from Atomic Force Microscopy and X-ray diffraction studies. In: Methods: A Companion to Methods in Enzymology. Macromolecular Crystallization (Ed. A. McPherson), Elsevier Inc, San Diego, vol.34, 273-299.

A.J. Malkin and A. McPherson (2004). Probing of crystal interfaces and the structures and dynamic properties of large macromolecular ensembles with in situ atomic force microscopy. In: Nanoscale structure and assembly at solid-fluid interfaces. (Eds. X.Y. Lin and J.J. DeYoreo). Plenum/Kluwer Academic Publisher, vol.2, 201-238.

A.A. Chernov, L.N. Rashkovich, I.L. Smol'skii, Yu.G. Kuznetsov, A.A. Mcrtchan and A.J. Malkin (1988). Growth of KDP - Group crystals from solutions. In: Growth of crystals, vol.15. Consultant Bureau Plenum, Publ. Co. New York, 43 – 91.


Invited Reviews

A. McPherson, Yu. G. Kuznetsov, A.J. Malkin, and M. Plomp (2003). Macromolecular crystal growth as revealed by atomic force microscopy applications in macromolecular crystallography. Journal of Structural Biology 142, 32-46 (Cover article).

A.J. Malkin, M. Plomp and A. McPherson (2002) Growth processes in macromolecular crystallization. Journal of Japanese Society of Microgravity Applications 19 (1) 14-18.

A. McPherson, A.J. Malkin, Yu. G. Kuznetsov and M. Plomp (2001). Atomic force microscopy applications in macromolecular crystallography. Acta Crystallographica D57, 1053-1060 .

Yu. G. Kuznetsov, A.J. Malkin, R. W.Lucas, M. Plomp and A. McPherson (2001). Imaging of viruses by atomic force microscopy. Journal of General Virology 82, 2025-2034 (Cover article).

A. McPherson, A.J. Malkin and Yu.G. Kuznetsov (2000). Atomic force microscopy in the study of macromolecular crystal growth. Annual Review of Biophysics and Bimolecular Structure 29, 361-410.

A. McPherson, A.J. Malkin and Yu. G. Kuznetsov (1995). The science of macromolecular crystallization. Structure 3, 759 –768.


Peer Reviewed Papers

C. J. Doona, F. E. Feeherry, K. Kustin, G. G. Olinger, P. Setlow, A. J. Malkin, T. Leighton (2015). Fighting Ebola through novel decontamination technologies for the military. Frontiers in Microbiology, 6:663. doi: 10.3389/fmicb.2015.00663.

M. Plomp, C. Monroe, P. Setlow and A.J. Malkin (2014). Architecture and assembly of the Bacillus subtilis spore coat. PLoS ONE 9(9): e108560. doi: 10.1371/journal.pone.0108560.

Doona, C. J., Feeherry, F. E., Setlow, P., Malkin, A. J., Leighton, T. J. (2014). The Portable Technologies for the Military. J. Vis. Exp. (88), e4354, doi: .3791/4354.

C.I. Lacayo, A.J. Malkin, H.-Y. Holman, L. Chen, S.-Y. Ding, M.S. Hwang and M.P. Thelen (2010). Imaging cell wall architecture in single Zinnia elegance tracheary elements. Plant Physiology 154, 1-13 (Cover article).

M. Plomp and A.J. Malkin (2009). Mapping of proteomic composition on the surfaces of Bacillus spores by atomic force microscopy-based immunolabeling. Langmuir 25, 403-409.

C. Monroe, M. Plomp, A.J. Malkin and P. Setlow (2008). Protozoal digestion of coat-defective Bacillus subtillis spores produces "rinds" composed of insoluble coat protein. Applied and Environmental Microbiology, 74, 5875-5581.

S. Ghoshi, B. Setlow, P.G. Wahone, A.E. Cowan, M.Plomp, A. J. Malkin and P.Setlow (2008). Characterization of spores of Bacillus subtilis that lack most coat layers, Journal of Bacteriology 190, 6741-6748.

M. Plomp, J. M. McCaffery, I. Cheong, X. Huang, C. Bettegowda, K. W Kinzler, S. Zhou, B. Vogelstein and A. J. Malkin (2007). Spore coat architecture of Clostridium novyi-NT spores. Journal of Bacteriology 189, 6457-6468.

M. Plomp, T. J. Leighton, K. E. Wheeler, H.D. Hill and A. J. Malkin (2007). In vitro high-resolution structural dynamics of single germinating bacterial spores. Proceeding of the National Academy of Sciences of the USA 104, 9644-9649.

M. Plomp, T. J. Leighton, K. E. Wheeler, M. E. Pitesky and A. J. Malkin (2005). Bacillus atrophaeus outer spore coat assembly and ultrastructure. Langmuir 21, 10710-10716.

M. Plomp, T. J. Leighton, K. E. Wheeler and A. J. Malkin (2005).Architecture and high-resolution structure of Bacillus thuringiensis and Bacillus cereus spore coat surfaces. Langmuir 21, 7892-7898.

A. J. Malkin, M. Plomp, T. J. Leighton, A. McPherson and K.E. Wheeler (2005). Unraveling the architecture and structural dynamics of pathogens by high-resolution in vitro Atomic Force Microscopy. Microscopy and Microanalyses, 32-35. doi: 10.1017/S1431927605050828, Published online by Cambridge University Press 30 Dec 2005.

Y.G. Kuznetsov, D. L. Makino, A. J. Malkin and A. McPherson (2005). The incorporation of large impurities into virus crystals. Acta Crystallographica D61, 720-723.

P.V. Zinin, V.L. Solozhenko, A.J. Malkin and L.C. Ming (2005). Atomic force microscopy studies of cubic BC2N, a new superhard phase. Journal of Materials Science 40, 309-311.

M. Plomp, T. J. Leighton, K. E. Wheeler and A. J. Malkin (2005). Bacillus spore coat ultrastructure, assembly and environmental dynamics. Scanning 27, 2, 97-98.

M. Plomp, T.J. Leighton, K.E. Wheeler and A. J. Malkin. (2005). The high-resolution architecture and structural dynamics of Bacillus spores. Biophysical Journal 88, 603-608.

A. McPherson, Yu. G. Kuznetsov, A.J. Malkin and M. Plomp. (2004). Macromolecular crystal growth investigations using atomic force microscopy. Journal of Synchrotron Radiation 11, 21 -23.

M.Plomp, A. McPherson and A.J. Malkin (2003). Repair of impurity-poisoned protein crystal surfaces. Proteins: Structure, Function and Genetics 50, 486-495.

A.J. Malkin, A. McPherson and P.D. Gershon (2003). Structure of intracellular mature vaccinia virus visualized by in situ AFM. Journal of Virology 77, 6332–6340.

A. J. Malkin, M. Plomp and A. McPherson (2002). Application of atomic force microscopy to studies of surface processes in virus crystallization and structural biology. Acta Crystallographica D58, 1617-1621.

A.J. Malkin and A. McPherson. Novel mechanisms for defect formation and surface molecular processes in virus crystallization (2002). Journal of Physical Chemistry 106, 6718-6722.

M. Plomp, M.K. Rice, E.K. Wagner, A. McPherson and A.J. Malkin (2002). Rapid visualization at high resolution of pathogens by atomic force microscopy: Structural studies of Herpes Simplex Virus-1. American Journal of Pathology 160, 1959-1966.

M. Plomp, A. McPherson and A.J. Malkin (2002) Crystal growth of macromolecular crystals: correlation between crystal symmetry and growth mechanisms. Journal of Crystal Growth 237, 306-311.

A.J. Malkin, Yu.G. Kuznetsov and A. McPherson (2001). Viral capsomer structure, surface processes and growth kinetics in the crystallization of macromolecular crystals visualized by in situ atomic force microscopy. Journal of Crystal Growth 232 173-183.

M.Plomp, A.McPherson, S.B. Larson and A.J. Malkin (2001). Growth mechanisms and kinetics of trypsin crystallization. Journal of Physical Chemistry B 105, 542-551.

Yu.G. Kuznetsov, A.J. Malkin and A. McPherson (2001). Growth kinetics and diffraction properties of STMV crystal. Proceedings of Materials Research Society Mtg., San Francisco, April 24-28, 2000, Vol. 620 (2001).

Yu.G. Kuznetsov, A.J. Malkin and A. McPherson, A. (2001). Self-repair of biological fibers catalyzed by the surface of a virus crystal PROTEINS: Structure, Function and Genetics 44, 392-396.

Yu.G. Kuznetsov, A.J. Malkin and A. McPherson (2001). The liquid protein phase in crystallization: A case study intact immunoglobulins. Journal of Crystal Growth 232, 30-39.

Yu.G. Kuznetsov, A.J. Malkin, and A.McPherson (2001). The influence of precipitant concentration on macromolecular crystal growth mechanisms. Journal of Crystal Growth 232, 114-119.

Yu.G. Kuznetsov, A.J. Malkin, R. Lucas and A. McPherson (2000). Atomic force microscopy studies of icosahedral virus crystal growth. Colloids and Surfaces 19, 333-344.

Yu.G. Kuznetsov, J. Konnert, A.J. Malkin and A. McPherson (1999). The advancement and structure of growth steps on thaumatin crystals visualized by atomic force microscopy at molecular resolution. Surface Science 440, 69-80.

A.J. Malkin, Yu.G. Kuznetsov, R.W. Lucas and A. McPherson (1999). Surface processes in the crystallization of turnip yellow mosaic virus visualized by Atomic Force Microscopy. Journal of Structural Biology 127, 35-43.

Yu.G. Kuznetsov, A.J. Malkin, and A. McPherson (1999). AFM Studies on the Mechanisms of Nucleation and Growth of Macromolecular Crystals. Journal of Crystal Growth 196, 489-502.

A. McPherson, A.J. Malkin, Yu. G. Kuznetsov, S. Koszelak, M. Wells, G. Jenkins, J. Howard and G. Lawson (1999). The effects of microgravity on protein crystallization: Evidence for concentration gradients around growing crystals. Journal of Crystal Growth 196, 572-586.

A. J. Malkin, Yu.G. Kuznetsov and A. McPherson (1999). In situ atomic force microscopy studies of surface morphology, growth kinetics, defect structure and dissolution in macromolecular crystallization. Journal of Crystal Growth 196, 471-488.

T-P. Ko, J. Day, A.J. Malkin and A. McPherson (1999). The structure of orthorhombic crystals of beef liver catalase. Acta Crystallographica 55, 1383-1394.

Yu.G. Kuznetsov, A.J. Malkin and A. McPherson (1998). Atomic force microscopy studies of phase separations in macromolecular systems. Physical Review B 58, 10, 6097-6103.

Yu.G. Kuznetsov, A.J. Malkin and A. McPherson (1997). Atomic force microscopy studies of living cells: Visualization of motility, division, aggregation, transformation and apoptosis. Journal of Structural Biology 120, 180-191.

Yu. G. Kuznetsov, A.J. Malkin, T.A. Land, J.J DeYoreo, A.P. Barba and A. McPherson (1997). Molecular resolution imaging of macromolecular crystals by atomic force microscopy. Biophysical Journal, 72, 2357-2364.

J.D. Ng, Yu. G. Kuznetsov, A.J. Malkin, G. Keith, R. Giege and A. McPherson (1997). Visualization of nucleic acid crystal growth by atomic force microscopy. Nucleic Acids Research 25, 2582 – 2588 (Cover Article).

A.J. Malkin, Yu. G. Kuznetsov and A. McPherson (1997). An in situ AFM investigation of catalase crystallization. Surface Science 393, 95 –107.

A. McPherson, Yu. G. Kuznetsov, A. Greenwood, J.D. Ng, A.P. Barba de la Rosa and A.J. Malkin (1997). Atomic force microscopy investigations of macromolecular crystal growth. Scanning, 19, 140-141.

A. McPherson, A.J. Malkin, Yu.G. Kuznetsov and S. Koszelak (1996). Incorporation of impurities into macromolecular crystals. Journal of Crystal Growth 168, 74-92.

A.J. Malkin, Yu.G. Kuznetsov and A. McPherson (1996). Defect structure of macromolecular crystals. Journal of Structural Biology 117, 124-137 (Cover article).

Yu. G. Kuznetsov, A.J. Malkin, W. Glantz and A. McPherson (1996). In situ atomic force microscopy studies of protein and virus crystal growth. Journal of Crystal Growth 168, 63-73.

A.J. Malkin, Yu. G. Kuznetsov, and A. McPherson. Incorporation of microcrystals by growing protein and virus crystals (1996). Proteins 24, 247-252.

Yu. G. Kuznetsov, A.J. Malkin, A. Greenwood and A. McPherson. Michelson interferometric studies of protein and virus crystallization (1996). Journal of Crystal Growth 166, 913-918.

T.A. Land, A.J. Malkin, Yu. G. Kuznetsov, A. McPherson and J. J. DeYoreo (1996). Mechanisms of protein and virus crystal growth: An atomic force microscopy study of canavalin and STMV crystallization. Journal of Crystal Growth 166, 893-899.

A.J.Malkin, Yu.G. Kuznetsov, W.Glantz, and A. McPherson (1996). Atomic force microscopy studies of surface morphology and growth kinetics in thaumatin crystallization. Journal of Physical Chemistry 100, 11736-11743.

A.J. Malkin, Yu. G. Kuznetsov, T.A. Land, J.J. DeYoreo and A. McPherson (1995). Mechanisms of growth for protein and virus crystals. Nature Structural Biology 2, 956-959.

Yu. G. Kuznetsov, A.J. Malkin, A. Greenwood and A. McPherson (1995). Interferometric studies of growth kinetics and surface morphology in macromolecular crystal growth. Canavalin, thaumatin and turnip yellow mosaic virus. Journal of Structural Biology 114, 184 – 196.

A.J. Malkin, T. A. Land, Yu. G. Kuznetsov, A. McPherson and J. J. DeYoreo (1995). Investigation of virus crystal growth by in situ atomic force microscopy. Physical Review Letters 75, 2778 – 2781.

T. A. Land, A.J. Malkin, Yu. G. Kuznetsov, A. McPherson and J. J. DeYoreo (1995). Mechanisms of protein crystal growth: An atomic force microscopy study of canavalin crystallization. Physical Review Letters 75, 2774 – 2777

A. McPherson, S. Koszelak and A.J. Malkin (1995). A perspective on macromolecular crystal growth in microgravity. Proceedings of the International Aerospace Congress, pp. 191 - 194. (Eds. P.K. Crouch and V.I. Polezhaev) Moscow, Russia.

A.J. Malkin and A. McPherson (1994). Nucleation phenomena and kinetics of crystallization in macromolecular systems. Acta Crystallographica D50, 385 – 395.

A.J. Malkin, J. Cheung and A. McPherson (1993). Crystallization of satellite tobacco mosaic virus. I. Nucleation phenomena. Journal of Crystal Growth 126, 544 – 554.

A.J. Malkin and A. McPherson (1993). Crystallization of satellite tobacco mosaic virus. II. Postnucleation events. Journal of Crystal Growth 126, 555 – 564.

A.J. Malkin and A. McPherson (1993). Light scattering investigations of the protein and virus crystal growth: ferritin, apoferritin and satellite tobacco mosaic virus. Journal of Crystal Growth 128, 1232 – 1235.

A.J. Malkin and A. McPherson (1993). Crystallization of pumpkin seed globulin: growth and dissolution kinetics. Journal of Crystal Growth 133, 29 – 37.

A.J. Malkin, Yu. G. Kuznetsov and I.V. Alekseev (1989). Two-dimensional growth of ADP crystals. In: Proceedings of the 11 International Symposium on industrial crystallization. (Garmash-Partenkirchen, West Germany), pp. 411 – 415.

A.J. Malkin, A.A. Chernov and I.V. Alekseev (1989). Two-dimensional nucleation. Dipiramidal face of ADP crystals. Soviet Physics – Crystallography 34, 581-584.

A.J. Malkin, A.A. Chernov and I.V. Alekseev (1989). Growth of dipiramidal face of dislocation-free ADP crystals. Free energy of steps. Journal of Crystal Growth 97, 765-770.

A.A. Chernov and A.J. Malkin (1988). Kinetics of formation of stoppers preventing growth of the (101) faces of ADP in aqueous solution. Soviet Physics – Crystallography 33, 885 – 887.

A.A. Chernov and A.J. Malkin (1988). Regular and irregular growth and dissolution of (101) ADP faces under low supersaturations. Journal of Crystal Growth 92, 432 – 444.

A.A. Chernov, A.J. Malkin and I.L. Smol'skii (1987). Kinetics of dislocation growth of dipyramid faces of ADP crystals at low supersaturations. Soviet Physics-Crystallography 32, 883 – 886.

A.A. Chernov, A.J. Malkin and I.L. Smol'skii (1987). Solution and growth kinetics of dipyramid face of ADP. Soviet Physics-Crystallography 32, 886 – 889.

A.J. Kogan, J.D. Gussak, V.I. Gusev and A.J. Malkin(1986). System for digital processing of data for the investigation of the crystal growth kinetics. Instruments and experimental technique 5, 231-232.

I.L. Smol'skii, A.J. Malkin and A.A. Chernov (1985). Laser interference X-ray spectrometer for investigation of growth of crystal faces from solutions. Soviet Physics-Crystallography 30, 331 – 333.

I.L. Smol'skii, A.J. Malkin and A.A. Chernov (1985). Kinetics and irregularity of growth of prism and dipyramid faces of ADP crystals. Soviet Physics-Crystallography 31, 454-457.

G.M. Popovich, V.I. Shekhobalova and A.J. Malkin (1983). Thermal stability of silver atoms in γ-irradiated silver-containing zeolites. Russian Journal of Physical Chemistry 57, 2199 – 2202.

G.M. Popovich, V.I. Shekhobalova and A.J. Malkin (1983). Stabilization of silver atoms in silver-zeolite systems. Russian Journal of Physical Chemistry 57, 2194 – 2198.


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