Chalk Talks

2016 May 05

Origins Chalk Talk -The Beagle in a Flask: Accessing artifacts of life’s evolutionary history through ancient-modern hybrid organisms - Betül Kaçar - OEB

9:00am

Location: 

Naito Laboratory, Room 205, 12 Oxford St, Cambridge

Abstract - Our living world is the result of a complex history spanning billions of years. Scientists have access to artifacts of this history, namely the fossil record and the genomes of many different living organisms. But there are surprisingly limited means with which to infer critical evolutionary elements in the deep past that resulted in modern biota. It is particularly difficult to reconcile (sometimes cryptic) fossil morphology on one hand, and genetic composition and diversification over time on the other, when so little about the behavior of ancestral organisms can be...

Read more about Origins Chalk Talk -The Beagle in a Flask: Accessing artifacts of life’s evolutionary history through ancient-modern hybrid organisms - Betül Kaçar - OEB
2016 Apr 07

Origins Chalk Talk- Inorganic Chemistry does logic and computes- Marta Dueñas (EPS- Pérez-Mercader Group)

9:00am

Location: 

Naito Laboratory, Room 205, 12 Oxford St, Cambridge

Abstract - 

Information processing is fundamental to life: metabolism, replication, evolution, etc all rely on it. Extant living systems carry out information processing chemically, using biochemistry. Chemistry-based computation is key to the information processing taking place in life. The most powerful, and yet simple, known construct in computation is the Turing machine. It consists of a finite state machine capable of giving unique responses to inputs from an infinite tape on which it can also write and erase. A Turing machine emulates a mathematician carrying...

Read more about Origins Chalk Talk- Inorganic Chemistry does logic and computes- Marta Dueñas (EPS- Pérez-Mercader Group)
2016 Mar 03

Origins Chalk Talk -A Statistical Mechanical Description of Nonenzymatic Replication- Albert Fahrenbach (MGH - Szostak Lab)

9:00am

Location: 

Naito Laboratory, Room 205, 12 Oxford St, Cambridge

Abstract- I will attempt to give an overview of some basic principles involved in nonenzymatic (RNA) replication using the language of statistical mechanics.  I will give a mathematical definition of fidelity in terms of thermodynamic and kinetic constants,  and try to demonstrate the connection between entropy and the transmission of information in this context.  My main goal is to try to convey a general idea of nonenzymatic replication using the language of physics, rather than specific chemical structures, in an effort to gives those non-chemists/biologists in the...

Read more about Origins Chalk Talk -A Statistical Mechanical Description of Nonenzymatic Replication- Albert Fahrenbach (MGH - Szostak Lab)
2016 Feb 04

Origins Chalk Talk - Understanding the Nearby Small Stars as Hosts of Planetary Systems - Jason Dittman (Astronomy- Charbonneau Group)

9:00am

Location: 

Naito Laboratory, Room 205, 12 Oxford Street, Cambridge

Abstract:

The nearby low-mass stars are the best candidate hosts for searching for transiting exoplanets to enable future characterization of their atmospheres. Unfortunately, our understanding of exoplanets is most often limited by our ability to characterize the host star. In this talk, I will focus on this stellar characterization problem, and how the MEarth transit survey has enabled us to better understand these stars. MEarth consists of 2 arrays of 8 telescopes each, one located at Mt. Hopkins, Arizona, and the other at Cerro Tololo, Chile. First, I used data from the...

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2015 Dec 03

Origins Chalk Talk "A Simple Analytical Model for Rocky Planet Interior" Li Zeng (EPS- Jacobsen Group)

9:00am

Location: 

Naito Laboratory, Room 205, 12 Oxford St, Cambridge

Abstract:
From PREM (Dziewonski & Anderson 1981), I deduce a simple analytical model for rocky planets. Tested with PREM-extrapolated numerical models (Zeng, Sasselov, Jacobsen 2015), this model can be applied to any two-layer (iron-silicate) rocky exoplanets with CMF (core mass fraction) range 0.2∼0.35 and mass range of 0.1~20 M⊕. This analytical model yields several handy and powerful formulae for the interior of such a planet. They can provide physical insights into the planet structure. 

2015 Nov 05

Origins Chalk Talk - David Glenn (Physics - Walsworth Group)

9:00am

Location: 

Naito Laboratory, Room 205, 12 Oxford St, Cambridge

Abstract: I will describe recent work on the development of a sensitive magnetic-field microscope with sub-micrometer spatial resolution. This instrument employs a layer of nitrogen-vacancy (NV) color centers at the surface of a diamond chip to enable imaging of magnetic fields from nearby samples. Together with collaborators in the MIT department of Earth, Atmospheric and Planetary Sciences, we have used the NV-diamond microscope to study distributions of magnetic minerals in a variety of terrestrial and meteoric rocks. The combination of spatial resolution and magnetic sensitivity of our...

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2015 Oct 01

Origins Chalk Talk - Gregory Henkes (EPS-Pearson Group) - Biomarkers from photosynthetic organisms as geologic recorders of ocean biogeochemistry

9:00am

Location: 

Naito Laboratory, Room 205, 12 Oxford St, Cambridge

Abstract: Organic molecules preserved in sedimentary rocks are generally regarded as robust recorders of the biology and chemistry of ancient environments. Here I will outline our recent efforts to extract, quantify, and measure the isotopic composition of compounds derived from chlorophyll molecules in organic-rich rocks. Their nitrogen stable isotope compositions are of particular interest because they record fingerprints of ancient ocean biogeochemistry that are not found in modern seas. Hypotheses for these observations include enhanced ammonium recycling and redox control on the...

Read more about Origins Chalk Talk - Gregory Henkes (EPS-Pearson Group) - Biomarkers from photosynthetic organisms as geologic recorders of ocean biogeochemistry
2015 May 21

Chalk Talk - Alán Aspuru-Guzik, Professor of Chemistry and Chemical Biology

9:00am

Location: 

Naito Laboratory, Room 205, 12 Oxford St

Abstract - My group members and myself are interested in the energy cycles of prebiotic molecular networks and metabolism. To be able to explore such networks, we have developed methods that combine heuristic reaction rules with quantum chemical calculations to be able to explore quickly the highly-dimensional potential energy surfaces associated with these reactions. We have explored the formose reaction and compared its network properties to those of metabolic networks. We also have explored the non-enzymatic reverse tricarboxilic acid cycle to determine its uniqueness amongst other...

Read more about Chalk Talk - Alán Aspuru-Guzik, Professor of Chemistry and Chemical Biology
2015 Mar 05

Chalk Talk -Mimicking the properties of Life with a Generic Stochastic Reaction-Diffusion System, Alberto Munuzuri (EPS - Perez-Mercader Group)

9:00am

Location: 

Naito Laboratory, Room 205, 12 Oxford Street

Life and living systems (LS) constitute the most complex class of natural phenomena that we know on Earth and, at least for now, in the Universe. Their functioning involves thousands of biochemical reactions and processes, all working at many different temporal and spatial scales. When it comes to understand Life and its properties, the traditional approach is to start from details and work from there to a full understanding of the complete system, i.e. a bottom-up process. In this talk we will discuss a completely different, but complementary, (top-down) approach. Starting from basic...

Read more about Chalk Talk -Mimicking the properties of Life with a Generic Stochastic Reaction-Diffusion System, Alberto Munuzuri (EPS - Perez-Mercader Group)
2015 Feb 05

Chalk Talk -Study on Bacterial Protein Synthesis System toward the Incorporation of D-Amino Acid - Po-Yi Huang (HMS- Church Group)

9:00am

Location: 

Naito Laboratory, Room 205, 12 Oxford Street

Abstract:Life is anti-entropic and highly organized phenomenon with two characteristics reinforcing each other: homochirality and the stereospecific catalysis of chemical reactions. The exclusive presence of L-amino acids and R-sugars in living world well depict this. Hypothetically, the amino acids and sugars of reverse chirality could form a parallel kingdom which is highly orthogonal to the present world. The components from this mirror kingdom, such as protein or nucleic acid, will be much more resistant to the defensive mechanism of present living system, which could be of great value...

Read more about Chalk Talk -Study on Bacterial Protein Synthesis System toward the Incorporation of D-Amino Acid - Po-Yi Huang (HMS- Church Group)
2015 May 07

Chalk Talk - "The Origin of the Moon and the Current Isotopic Crisis." Kun Wang (EPS - Jacobsen Group)

9:00am

Location: 

Naito Laboratory, Room 205, 12 Oxford Street

Numerical simulations have been used to support the hypothesis that the Earth-Moon system is the product of an ancient catastrophic Giant Impact event. The original simulations suggested that the Moon was made mostly from the impactor material with only minor contributions from the Earth. In contrast, isotopic studies have demonstrated that the Earth and Moon are remarkably similar in their isotopic compositions for many elements (e.g., O, Ti, Cr and W isotopic anomalies and Mg and Si stable isotopes). This similarity between the Earth and Moon is unique in our Solar System when...

Read more about Chalk Talk - "The Origin of the Moon and the Current Isotopic Crisis." Kun Wang (EPS - Jacobsen Group)
2015 Apr 02

Chalk Talk - Natural nuclear reactors as a case study for coupled thermodynamic feedback and organic synthesis in geological systems- Zachary Adam (EPS - Knoll Group)

9:00am

Location: 

Naito Laboratory, Room 205, 12 Oxford Street

Abstract:  Energy dissipation processes in abiotic systems is typically unidirectional, ranging from the gentle rain of sunshine to the explosive release of an impactor. Though these and other dissipation processes have served as invaluable prebiotic synthesis scenarios, the thermodynamics of such systems are inherently problematic for origins of life studies. Mass transport, thermal and chemical gradients converge and interact on short systemic scales to freeze reactants into organic matter, but work and information flow rarely result in stable circulatory patterns that link chemical...

Read more about Chalk Talk - Natural nuclear reactors as a case study for coupled thermodynamic feedback and organic synthesis in geological systems- Zachary Adam (EPS - Knoll Group)
2014 Nov 06

Chalk Talk - Dmitry Zubarev -CCB - Reconstruction of Prebiotic Reaction Networks

9:00am

Location: 

Naito Laboratory, Room 205, 12 Oxford Street
Abstract: The central ambition of theoretical chemistry is to describe chemistry in its diversity solely as a solution to Schrodinger Equation. The difficulty of this strategy is that it has to capture development of molecular systems at multiple spatiotemporal scales which is prohibitively 
expensive. Prebiological chemistry is the most challenging in this sense because the target phenomenon - the emergence of life - cannot be meaningfully represented as a collection of independent events at the level of organic reactions,...
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2014 Dec 04

Chalk Talk - Noam Prywes & Ben Adlam - On the Exploration of Evolutionary Landscapes

9:00am

Location: 

Naito Laboratory, Room 205, 12 Oxford Street

The evolutionary space of a single enzyme is far too large to explore systematically.  Despite this, there has been much success in the field of in vitro evolution, both from enzymes with starting activity and from random sequence.  What can we say about the structure of evolutionary space based on these findings?  What can we say about optimal methods for the discovery and improvement of enzymes?  Drawing on recent experimental and theoretical work we will go over several ways by which this problem has been approached in the past and will explore questions of how to...

Read more about Chalk Talk - Noam Prywes & Ben Adlam - On the Exploration of Evolutionary Landscapes
2014 Oct 02

Origins Chalk Talk - William Shih, Ph.D. (Wyss Institute-HMS) - 3D Digital Nanofabrication and Scaffolding of Lipids via DNA Self-Assembly

9:00am

Location: 

Naito Laboratory, Room 205, 12 Oxford Street

Abstract: A key challenge for nanotechnology is the programmable self-assembly of complex nanostructures. Our laboratory pioneered a versatile general solution: custom three-dimensional shapes, the size of small viruses, that can be conceived as stacked sheets woven from parallel DNA double helices. Current work is focused on achieving greater complexity via hierarchical self-assembly, and exploring site-specific chemical functionalization and programmable actuation. We also have been studying capture of lipid bilayers on the surface of DNA-origami nanostructures. One of...

Read more about Origins Chalk Talk - William Shih, Ph.D. (Wyss Institute-HMS) - 3D Digital Nanofabrication and Scaffolding of Lipids via DNA Self-Assembly

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